Sources of mouse L1 sequences

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Collections Nodal and Consensus

From GenBank, unless otherwise indicated.

AB10266A
- From AB10266
- Redundant with a match found in MMMHC29N7, AF030001, g2564945
- Mus musculus major histocompatibility locus class IIIregion.
- Compl. of 33150..32275 matches L1MdA2 6498..7377
- Falls in DA2 terminal burst.
AC2315A
- From AC002315,g2258164
- Chromosome X
- Compl. of 110079...108209 matches L1MdA2 5507...7377 99%
- Falls in DA2 lineage.
AC2315b
- From AC002315, g2258164
- 98028..99365 matches L1MdA2 6032..end
- No TSD identified
- Used in construction of ftenode1
AC2315r
- From AC002315, g2258164
- Mouse BAC-146N21 Chromosome X contains iduronate-2-sulfatase gene.
- 29292..30130 matches L1MdA2 6548..7380
- Falls in Z_lineage.
AC2315xa
- From AC002315, g2258164
- Chromosome X
- Compl.of 105331..103824 matches L1MdA2 5864..end 92%
- Falls in Y_lineage.
AC2406#1
- From AC002406, g298124
- Chromosome X
- Compl. of 893..1867 matches L1MdA2 6380..end 90%
- TSD = AAAGAAGGTGAGATTG @ 862/1884
- Falls in L2 lineage
AC2406#2
- From AC002406, g298124
- Chromosome X
- Compl.of 159298..158977 matches L1MdA2 7040..end 89%
- TSD = compl.of CATAGTG @ 158968/159297
- Falls in L2 lineage
AC2406A
- From AC002406,g2981248
- Chromosome X
- 20326..26207 matches L1MdA2 full body 1538..7363 96%
- May have TSD : AAGATTGACAATTGG @ 19951/26228
- F2406 type promoter @ 19964..20325 with 126bp extra sequences by triplication.
- Extreme 5' end appears in M-lineage and 3' end falls in top of DA2 lineage. The recombination point appears to be between 2940 and 2960 Loeb coordinates.
- Other F2406 promoters:
  - AC003996 20486..20697;
  - MMHC438n12 42795..42589;
  - MMAE000665 45515..45719;
  - MMAE000664 235174..235408;
  - AC004407B
  - AC005403A
AC2406B
- From AC002406, g298124
- 50328..51554 to A2 6154..7380.
- Maps to A2 lineage.
- No TSDs apparent
AC2406D
- From AC002406
- 87467..93460 includes a full length body and partial F-type promoter.
- TSD not identified.
- Falls with MML1FTE on 3' end tree, but does not join it.
- 5' end appears to fall near top of M lineage, then switches to main lineage just below mmL1FTE at around 3550.
- Partial F-type promoter 87467..87611 does not have the characteristic deletion of the fte m1 F promoters.
AC2406E
- AC002406E was interrupted at A2 coordinate 6098 by insertion of a younger inverted bipaitite L1. The 3'ends of the 2 L1's subsequently underwent recombination. Only the portion listed above is nonrecombinant.
- Compl.of 159683..164802 matches L1MdA2 F promoter..6098
- Original TSD = CCCCTCCACTATGCT @ 158962/164800
AC3019a
- From AC003019, g3868739
- Mus musculus Chromosome 4 BAC clone BacB6.
- 71834..74385 matches L1MdA2 4824..7376
- Falls DA2 lineage.
AC3019r
- From AC003019, g3868739
- Mus musculus Chromosome 4 BAC clone BacB6.
- 4363..2427 matches L1MdA2 5441..7376
- Falls in Z_lineage.
AC3019rb
- From AC003019, g3868739
- Mus musculus Chromosome 4 BAc clone BacB6.
- 83268..82339 matches L1MdA2 6449..7377
- Falls in Z_lineage.
AC3063A
- Marker results available.
AC3949#1
- From AC003949, g3287717
- Mus musculus chromosome 19, clone D19-96,B7.
- Compl of 6155..65173 matches L1MdA2 3671..7376
- Falls in top of L2 lineage.
AC3949lr
- From AC003949, g3287717
- Mus musculus chromosome 19, clone D19-96, B7.
- 26656..25421 matches L1MdA2 6142..7377 95%
- Falls in T_F lineage, T_F1 subfamily.
- 3' transduced segment 25278..25415
- TSD = AACAGAGAATTCT @ 25262/26657
- Repeatmasker says inserted in Lx4 repeat.
AC3995a
- From AC003995
- AC003995 Compl. of 16..5920 matches full body of L1MdA2 with a small section of F-type promoter
- No TSD identified
- Used in construction of ftenode1
AC003996, g2772523, clone ma66a097, TCR alpha locus
- 3893 bp of 5' end overlapped by AC004096, ma66a907
- AC3996r
  - 40500..43808 (3' end) matches L1MdA2 3731..7047
  - 3' end in AC005938: fuse 17848..18175
  - Inserted in A run with CAA motif; TSD obscured.
  - Falls in Z_lineage.
- AC3996b
  - body: 20856..27205 + strand to A2 1562..7359
  - putative M type promoter 20315..body
  - TSD=AAAGAATGGCCTC @ 20299/27254
  - short USC
AC3997
- From AC003997, g2772522
- Mouse BAC mbac20 from 14D1-D2 (T-Cell Receptor Alpha Locus)
- 35393..29226 matches L1MdA2 1201..7377
- Falls in DA2 lineage.
AC004096, g2828224, TCR alpha locus, ma66a100
- 5' end overlapped by AC003995, ma66a094
- AC4096A
  - 27293..33543 matches L1MdA2 A promoter (1166)..7377 98%
  - Promoters are Schichman A type II-II-IV
  - TSD at 27282/33566 = ataactatccc
  - Compound p(A) tail: AATAAAAAATGGA₉GAATTTTTCTA₁₀TA
  - Falls in middle of DA2 lineage
AC4101
- From AC004101, AC004101 ,g2828223
- Mouse Cosmid
- Redundant with AC5240a found in AC005240.
- Compl. of 27888..22478 matches full body of L1MdA2 97%
- A type promoter array at 27889..28661.
  - Promoter types are Schichman's A-type IVb,IVb
- Possible TSD, but is obscured by insertion within a GGA_n tract.
- Falls at very top of DA2 lineage.
AC004399, g2951970, ma03m061, TCR alpha locus
- 5' end overlapped by AC005938, ending within L1 AC4399a
- AC4399A
  - 3707..10050 matches L1MdA2 A promoters (1032)..7375 99%
  - A-type promoters of Schichman type I₂-IV.
  - TSD at 3690/10053 aaaagaaaaaagaaagtg
  - Falls in middle of DA2 lineage.
AC004405, g2957158, TCR alpha cluster, clone ma36a240
- 5' end overlaps mbac6, AC004407
- AC4405A
  - Compl.of 26048..27508 matches L1MdA2 5917..7377 99%
  - Possible TSD obscured by insertion in poly(A) tract
  - Falls in DA2 lineage.
- AC4405B
  - 14272..7869 Compl. of A2 1001(A promoter)..3' end
  - Promoters are Schichman type II-II-IV
  - TSD @ 7848/14273 = gatgattggttt(g/a)
  - Falls in middle of DA2 lineage
- AC4405AD
  - 5' end from 37638..43178 in AC004405 matches A2 849..6389; 99%
  - 3' end from 1..2452 AC005240 matches A2 4927..7377(end); 99%
  - promoter type is Schichman I-I-I-III
  - In terminal burst on DA2 lineage
- AC4405lr
  - 18156..24786 matches L1MdA2 744..7377
  - It is a recombinant at about position 5704 with a full length A2 lineage element. The 5'side falls in A2 lineage and 3' side falls in TF lineage.
    - TF part: 23113..24786
    - A2 lineage part (Ac4405rec): 18156..23112
AC004407, mbac6, TCR alpha locus, g2957156
- 3' end overlaps ma36a240, AC004405
- AC4407a
  - AC004407 42483..48169 matches L1MdA2 1562.. end
  - F-type promoters in region 42075..42483.
  - missing 3' end may appear at 55031..55141, but there is no clear evidence that this segment is from the same initial insert.
  - No TSD identified
  - Used in construction of ftenode1
- AC4407r
  - 103184..101271 matches L1MdA2 5465..7377
  - Falls in Z_lineage.
AC5240A
- From AC005240, g3287703
- Falls in duplicated chromosomal region of T alpha cluster such that this sequence is redundant with AC4101a.
- Compl.of 41330..35927 matches L1MdA2 1966..7377 97%
- The promoter segment is on the 5' end of AC004406
- Falls in top of DA2 lineage
AC5240B - See AC4405AD
AC005403, clone ma53a068, g3402732, TCR alpha cluster
- 3' end overlaps mbac53gap, AC005963 to base 49.
- AC5403A
  - 26212..28200 matches 3 F-type promoter monomers + A2 body..3153.
  - Closely matches AC4407B, including about 3kb of flanking sequence upstream of the F promoter array. So this is a duplicated unit within the T alpha cluster.
  - Illegitimate recombinant with another L1 on the 3' side.
- AC5403lr
  - Inverted bipartite structure
    - 3' seg: 11691..13702 matches L1MdA2 5366..7377; 96%
    - 5' seg: 10649..11690 compl A2 4328..5396; 97%
  - May have TSD composed of oligo A.
  - Falls in TF lineage
- AC5403C
  - 1..281 matches A2 7097..7377 93%
  - 5' cut off in clone
  - Falls in T_F
AC5413a
- From AC005413, g3850602
- Full length L1 with A type promoter
- Compl. of 12440..19207 matches L1MdA2 612..7380
- TSD=compl. of CAATTTTCAACTTTAT @ 12428/19207
- Falls in A2 lineage at bottom
- Redundant with a L1 in overlapping entry AC005665
AC5413b
- From AC005413, g3850602
- Full length L1 with A type promoter
- 56462..62842 matches L1MdA2 promoter..7380
- TSD=AAAAGATGCCAAAGTC
- Falls on top of A2 lineage near AC2406a
- Redundant with a L1 in overlapping entry AC005665
AC5665r
- From AC005665, g3687270
- Mus musculus chromosome 17 BAC clone citb76k14 from the MHC region.
- 17162..17881 matches L1MdA2 5596..7377
- Falls in Z_lineage.
AC5743A
- From AC005743, g4246254
- full len A/F comp. element
- body: 127827..133461 matches A2 1723..end
- F promoter portion: 127694..127827
- A promoter portion: 127404..127693
- TSD not identified
AC005835, g3776583, TCR alpha locus, mbac 84
- AC003993 is included at 3659..41935
- AC5835A
  - TSD at 109149 and 115831: AAGATTGCAAATT
  - Full length 3 1/2 TF promoters
  - Falls in Z_lineage.
- AC5835b
  - full length with TF-like promoter array
  - TSD=AAAGAGCGCTGTGG @ 89539/96544
  - Interrupted by IAP LTR at 90779..91143
  - TF promoter array at 89559..90317
  - Z lineage ?
AC005938, g3845391, TCR alpha locus, chrom 14, clone= mbac24 or RG:200p8
- A-type L1 truncated at 3' end is same as L1 AC4399a
- AC5938A
  - From AC005938, g3845391
  - Mus musculus chromosome 14 clone UWGC:mbac24 or RG:200P8 map 14D1-D2.
  - Full length L1 with TF promoter(1 and 1/2)
  - 58491..64701 matches L1MdA2 1594..7377 + promoter
  - TSD = AGAAAACCAAGAGCA @ 58475/64711.
  - Falls in TF lineage.
- AC5938B
  - From AC005938, g3845391
  - chromosome 14 clone UWGC:mbac24 or RG:200P8 map 14D1-D2.
  - Full length L1 with TF promoter( 8 and 1/2)
  - 77205..84920 matches L1MdA2 1594..7377 + promoter
  - TSD = AAAGAAGTCTTTTTAC @ 77188/84921.
  - Falls in TF lineage.
- AC5938D
  - 14539..18175; See AC3996r
AC6289A
- From AC006289, g4096089
- Same bac sequenced as AF030001, clone 29n7
- 1..4349 neg. to A2 promoter..5506
- Additional sequence in overlapping entry AF050157 244863..243607 extends to A2 coordinate 6664
- 3' truncated, no TSD recognized
- maps in A2 lineage around 4101a
- Note: another L1 insert in AC006289 is redundant with AB10266a
AC6584A
- From AC006584, g4926837
- Full length L1 with TF promoter (5)
- 72305..77607 matches L1MdA2 1966..7268
- Simple sequence was found around 77701/70861 (GAAA) _n.
- Falls in Z lineage.
AC7049a
- From AC007049,
- 5415..4831 neg to A2 6778..end
- TSD = TATGTCTCCCTTTTC @ 4801/5416
- Inserted in AC7049b
- In mid A2 lineage above subst 7347 & below subst 7081.
AC7049b
- From AC007049,
- A-type element with A-type promoter
- Interrupted by AC7049a
- Interrupted by a deletion
- TSD = CCCATG(A/T)AATTCTTT @ 8234/4379
- Seg. 1 8232..5416 neg. to A2 1277..4075 (includes promoter)
- Seg. 2 4815..4751 neg. to A2 4061..4125
- Seg. 3 4753..4409 neg. to A2 7014..end
- High on A2 lineage, somewhere around L1Md9.
Ae664#1
- From MMAE000664, AE000664, AE000522
- TCR beta locus
- Compl. of 24995..250575 matches L1MdA2 6746..end 91%
- TSD: AGAAGTGAGGTTGAACAT @ 249936/250576
- Falls in L2 lineage
AE665a
- full length with M type promoter (2)
- 45530..51663 to A2 1562..7328 + it has promoter in this range
- Anchor of M lineage.
AE665xa
- From AE000665, AE000552, g2358100
- Mus musculus TCR beta locus.
- 30406..33113 matches L1MdA2 6670..end
- Falls in Y_lineage
AE665xc
- From AE000665, AE000552, g2358100
- Mus musculus TCR beta locus.
- 56311..57786 matches L1MdA2 5887..end
- Falls in Y_lineage.
AF21335A
- From AF021335, g2444469
- TCR gamma 2 and gene clusters.
- AF021335b inserted within; TSD of AF021335b at 17748/19086
- Seg 1 14784..17748 matches A2 + str promoter..4061.
- Seg 2 19087..22402 matches A2 + str 4062..end
- TSD = AAAAAGCTGGACCCAG @ 22417/14769
- Falls in DA2 lineage.
AF21335b
- From AF021335, g2444469
- Mus musculus T cell receptor gamma locus, TCR gamma 2 and gene clusters.
- 17762..19075 matches L1MdA2 6063..end
- TSD=GAAAAGGGAGACAT @ 17748/19086
- Inserted within AF21335a
- Falls in DA2 lineage.
AF37352a (aka. AFa)
- From AF037352, g2815645
- Compl.of 46025..52332 matches L1MdA2 full length body + 3 F promoter monomers.
- TSD =ACAAAATAGTATTTT @ 45988/52370
AF37352B (aka AFb)
- 89370..94756 + str A2 1967..end
- Continues with an A/F composite promoter
- Falls in L2 clade.
AF37352r
- From AF037352, g2815645
- TCR gamma 1 and gamma 3 gene clusters.
- 62345..61122 matches L1MdA2 6152..7376
- Falls in Z_lineage.
AF7574
- From AF007574, g2677832
- Mus musculus Y chromosomal repetitive DNA sequence.
- 1812..3075 matches L1MdA2 6110..7376
- Falls in DA2 lineage.
AF91216A
- From AF091216, g3851580
- Full length L1 with A type promoter (2 and 1/2)
- Compl. of 26410..20027 matches L1MdA2 1030..7377 98%
- Possible TSD = compl. of TTTCTTT @ 20023/26420
- Falls on DA2 lineage around MMconreg 1
AF136179a
- spermine synthase gene
- TSD= AGACTTAATTTT (on gb strand)
- 8947..9159 - str to A2 7147 .. end
- In TF.
AL031742, MMBAC45N8, g5304949
- Strain = 129/Sv
- AL31742a
  - full length A-type L1 from A2 terminal burst
  - 78516..72277 neg. strand to A2 1037..7359
  - TSD= CCATAGCCCACTTCTT on GenBank strand @ 72239/78517
Cas3
- From MMCASEIB, X13484, X15991, X15992, g50292
- Mouse DNA for beta-casein.
- 3302..3824 matches L1MdA2 6930..7362; 87%
- Falls in bottom of L2 lineage.
DAC
- Recovered by PCR
Igkwnp1
- From MUSIGKWNP, M28133, g197548
- Mouse germline Ig kappa chain gene v-1c region.
- 3150..4126 compl. of L1MdA2 6385..end; 5' end cut off.
- Falls in top of L2 lineage.
IL6A
- 5955..3879 comp. strand from MUSIL6A, M20572
- TSD ACAGCAGGAATCTT(T/A)TT(T/C)TCAA(T/A)TT @3854 AND 5970
- 85% to L1MdA2 5508..end.
- Above L1fte
L1Bg
- Perou et al., 1997.
- Falls in Z lineage
L1BstI
- From X03725, aka mmL1Bst1, MUSL1Bst1,
- 1..2729 + str to A2 1578..4308; 99%
- cloned internal L1 BstNI fragment
- Maps in A2 terminal burst
L1C105
- See Zhao, Y., et al., 1996
- Inverted bipartite:
  - 5'segment: compl. of 114..155
  - 3'segment: 155..860
- Covers A2 coordinates 6611..end.
- TSD = AAGTATGTAAAGGTAT @ 100/918
- Falls in Ms7024 lineage.
L1EL111
- See Rikke,B.A., et al., 1995
- Inverted bipartite:
  - 5'segment: compl. of 197..345 matches A2 6174..6322
  - 3'segment: 346..1417 matches A2 6330..end
- TSD = TAAAAAACTAATAA @ 185/1411
- Falls in Ms475 lineage.
L1EL2
- GenBank entry pending
- 5' segment: 272..1256 96% to A2 5887..6870
- 3' segment: 1257..1726 95% to A2 6892..7362
- has a 3' transduced region 1726..1967 counting the 2nd pA tail.
- TSD at 257/1968 = AGAAAAATCAGCTCAGG
- Flank to Flank and Flank to 5' end PCR marker results
L1FTE
- 449..6781 from MML1FTE, X57795
- Is full length prototypical old F-type L1.
- TSD still identifiable
- Has 3 F promoter monomers
- Similarity of body to L1MdA2 is 90%
L1Mc1
- From MUSL1MC1, L44128, g995609
- Mus caroli L1Mc1
- Inverted bipartite: Junction: ATGCCCTCCA/ATTGGACTTG -3' segment; Deletion: = 253 5' seg 24..366 matches L1MdA2 compl.of 6621..6963 90% 3' seg 367..512 matches L1MdA2 7216..7364 86%
- TSD = TCAAAAAAA @ 3/522
- Falls in L2 lineage
L1Md1
- From MMBGCXD, X14061, mouse beta globin cluster
- Compl. of 643..2395 from MMBGCXD
- Matches L1MdA2 5610..end 93%
- TSD identified
L1Md2
- From MMBGCXD, X14061, mouse beta globin cluster
- Is interrupted by L1Md8
- 3938..4165 + 4353..5598 in MMBGCXD
- Matches L1MdA2 5937..end
- TSD = AATTGCAAATTCA @ 3925/5597
L1Md3
- From MMBGCXD, X14061, g50150
- M.musculus beta-gloobin complex DNA.
- 25295..25927 matches L1MdA2 6745..7363 86%
- TSD = AAACCATCGGCTTTG @ 25281/25926
- Falls in bottom of L2 lineage
L1Md4
- From MMBGCXD, X14061, g50150
- 31,571-33617 matches A2 5316..7362 96%
- TSD at 31,557/33,660
- Was original prototype for L1Md4 clade
- Falls in TF, subset TF2
L1Md6
- From MMBGCXD, X14061, g50150
- Short L1 with TSD
- Has a USC
- 49475..50,182 matches L1MdA2 95% at 6630..7363
- TSDs at 49459/50324
- superficially in the same position as L1Mp-6, Burton et al., MBE 8:609-619(1991), in M. pahari (MUSL17244B), but really a separate insertion.
- Falls just above A2/L1Md4 split.
L1Md8
- From MMBGCXD, X14061, g50150
- Short L1 with TSD inside of L1Md2
- Compl.of 4171..4343 matches L1MdA2 7187..7363 88%
- TSD = TAAGGATAGTT @ 4156/4343
- Falls in L2 lineage
L1Md16
- From MMBGCXD, X14061, mouse beta-globin cluster
- Is an inverted bipartite element that is interrupted by another inverted bipartite element (L1Md17)
- 5' segment is 48,235..48,479 matching L1MdA2 6317..6568.
- 3' segment is compl. 45,440..46,269 + 48,227..48,236, matching L1MdA2 6568..end
- No TSD identified
L1Md17
- From MMBGCXD, X14061, mouse beta globin cluster
- Inverted bipartite element found within another L1 (L1Md16)
- 5' seg is 47,177..48,214
- 3' seg is compl. of 46,215..47.176.
- matches L1MdA2 5385..end
- TSD identified
L1MdA2
- Loeb et al., 1986
L1MdZ
- Kraft et al., 1992
- Compl. of 2371..3623 matches L1MdA2 7362..6110 95%; 5'end cut off at RI site.
- TSD not identified.
- Falls in Z_lineage.
L1_med
- Complement of sequence in fig. 5 of Kohrman et al., 1996
- Not in GenBank
- Sequence
- pA tail of approximately 100 bp.
- TSD = AATACTACAAAAGT (compl. of fig.)
- The mismatches indicated in fig. 5 are removed by a 2 base alignment gap representing a GG insertion.
- Probably in the Z family; the GG insertion matches L1Bg
L1Orl(aka L1 reeler)
- See Takahara et al, 1996and Naas et al, 1998
- Falls in TF lineage.
L1spa
- See Naas et al, 1998
- Falls in TF lineage. Prototype for L1spa sublineage.
M13164, Musbamhia, cloned L1 EcoRI frag.
- 1..1369 (whole file) + str. A2 4737..6115; 94%
- Maps around L1Md9
- 5' end, 5017, 5104, 5074, may be rec. seg. from DA2.
MMAE663A
- From MMAE000663, AE000663, g2358069
- TCR beta locus.
- Compl.of 115129..108548 matches L1MdA2 796..end.
- Falls in DA2 terminal burst.
- MMAE663A and MMAE663B were duplicated after the L1 insertion.
MMAE663B
- From MMAE000663, AE000663, g2358069
- TCR beta locus.
- 93600..100177 matches L1MdA2 796..end.
- Falls in DA2 terminal burst.
- MMAE663A and MMAE663B were duplicated after the L1 insertion.
MMAE663C
- From MMAE000663, AE000663, g2358069
- TCR beta locus.
- 30286..35698 matches L1MdA2 1967..7377
- Falls in DA2 lineage.
AE663r
- From MMAE000663, AE000663, AE000522, g2358069
- Mus musculus TCR beta locus from bases 1 to 250611.
- 136325..136659 matches L1MdA2 6624..6958
- Falls in Z_lineage.
MMAE664r
- From MMAE000664
- TCR beta locus
- 239179..240665 matches L1MdA2 + str 5887..end
- listed as part of a larger F-type L1 in GenBank annotation but there may be 3 independent L1s in the region 235411..240670.
- no TSD identified
- Falls in Z
Mmb2x1
- From MMB2RPT, X58283, g50108
- matches L1MdA2 6181..end
- Falls in bottom of L2 lineage
MMBAM05
- From MMBAM05, X00399, g50126
- An internal 0.5 kb L1 restriction fragment
- 28..276 matches L1MdA2 6035..6388 97%
- Falls in DA2 lineage.
Mmcax1
- From MMCASEIB, X13484, X15991, X15992, g50292
- Mouse DNA for beta-casein.
- Compl. of 776..1377 matches L1MdA2 7362..6778 90%
- TSD = TAAAGAAAACAAAA @763/1378
- Falls in Y_lineage.
MMCONREG-1
- From MMCONREG, Z13985, S50525, g50515
- M.musculus control region sequence DNA.
- 2060..3603 matches L1MdA2 5813..7362 96%
- TSD=AAGAAGACAGTGGAA @ 2046/3598.
- Falls in DA2 lineage.
Mmconreg2, MMcon2
- From MMCONREG, Z13985, g50515
- 8100..9592 matches L1MdA2 5878..7362 96%
- TSD = AAAAAAGGATACTC @ 8085/9605
- Falls in Z_lineage.
Mmlin
- From MMLINSAA, X13060, g52939
- Mouse musculus from BALB/c serum albumin gene truncated LINE-1 repeat in intron 12.
- 593..1410 matches 6544..7362 99%
- TSD identified. TSD=GAAAATGTTCCACG
- Falls in DA2 lineage.
- Population survey was conducted of this insert by Bellis et al., 1987
Mmonc
- From MMONCTLM, X52634, g53528
- MURINE flm ONCOGENE FOR tlm PROTEIN ORIGINALLY FROM BALB/c.
- Include 2 L1s. L1#1: Compl.of 1704..2649 matches L1MdA2 7127..6164 70% L1#2: Compl.of 2781..3250 (End) matches L1MdA2 7362..6893 99% 5' cut off. 1390/2763 9bp deletion.
- TSD identified for L1#1 AAAAAAAAAG @ 1399/2772
- Lane,M.A. and Tobin,M.B. Genomic sequence of the mouse oncogene tlm, Nucleic Acids Res. 18 (11), 3410 (1990)
- Falls in DA2 lineage.
Mmu15
- From MMU15647, U15647, g558906
- L1 cDNA from particle
- cut off 5' end and extends beyond P(A).
- 1/2 promoter 1..100 1..5939 matches L1MdA2 1439..7377 >99%
- Falls in DA2 lineage.
MMU22497
- From MMU22497, U22497, g1006781
- Mus musculus Int6-ps4 pseudogene.
- 1348..1608 matches L1MdA2 6638..6898 88%; 5' truncated 3' cut off L1
- Miyazadi,S. et al; The chromosomal location of the mouse mammary tumor gene Int6 and related pseudogenes in the mouse genome; Genomics 27(3), 420-424 (1995).
- Falls in L2 lineage.
Mmu82375
- From MMU82375, U82375, g2289098
- Mus musculus MSG2alpha, beta, gamma, delta and epsilon salivary protein (Vcs2) genes, complete cds.
- 17162..17881 matches L1MdA2 6657..7376
- Falls in Z lineage.
Mopc1
- From MUSMOPC, M11515, g199768
- Mus musculus (BALB/c) MOPC 41 plasmacytoma P-1-450 gene with a deletion replaced by a 2578 base pair insertion.
- 1..585 matches L1MdA2 5744..6326 99% 5' cut off
- TSD not identified.
- Kimura,S. and Nebert,D.W., Comparison of the mouse P(1)450 gene and flanking sequence MOPC41 plasmacytoma and normal liver, DNA 4 (5),365-375 (1985).
- Falls in DA2 lineage.
Mopc2
- From MUSMOPC, M11515,g199768. See "Mopc1" for general information.
- Compl. of 580..2570 matches L1MdA2 5542..3571 99%
- TSD not identified.
- Falls in DA2 lineage.
Muscy
- From MUSCY16B01, M60352, g192855
- Mouse testosterone 16a-hydroxylase type b (16aoh-b), exon 1.
- Lakso et al., Structures and characterization of sex specific mouse cytochrome p-450 genes as members within large family: Duplication boundary and evolution. Eur. J. Biochem. 195, 477-486, (1991).
- Compl. of 1..549 matches L1MdA2 6895..6343; 95% 3' cut offf before gene.
- Falls in Z_lineage.
Musec
- From MUSECDD, M11665, g102086
- L1 with TSD in extrachromosomal circle. Mus musculus thymocyte extrachromosomal circular DNA, clone MT104, R regino. Several L1's attributed to MT 104.
- 51..352 matches L1MdA2 7061..7362 98%
- TSD identified: AAAAAAAATTTA(A/G)AGG.
- Fujimoto,S. et al, Transposon-like sequences in extrachromosomal circular DNA mouse thymocytes, Proc. Natl. Acad. Sci. U.S.A. 82, 2072-2076 (1985).
- Falls in DA2 lineage.
Muska
- From MUSKAPG, M63707, g198562
- Mouse kidney androgen-regulated protein (DAP) gene.
- Compl.of 1..382 matches L1MdA2 6604..6223 98%, 3' cut off.
- Falls in DA2 lineage.
MusL1a1
- From MUSL1A1, M29324, g198644
- Mouse L1Md-A13 repetitive sequence.
- AKA L1Md-A13, A13
- Shehee, W R, et al. J Mol Biol 196, 757-767 (1987)
- 1105..7543 plus str. A2; >99%
- TSD = AACCTACCTCTAGC @ 1092/7477
- Falls in DA2 lineage.
Musmd
- From MUSMDRXX, M33580, g199113
- Mouse P-glycoprotein (mdr1a) gene, exons 1 and 2.
- 1..1252 matches L1MdA2 6110..end.
- TSD not identified.
- Falls in DA2 lineage.
Musmh
- From MUSMHH2CAS, M62844, g199407
- Mus musculus MHC class I (Haplotype CAS3) integral membrane protein M3 (H-2M3) gene, complete cds. 5' cut off and 3' truncated L1; 3' truncation probably a cloning artefact.
- Compl.of 4820..5599 (end) matches L1MdA2 7107..6110 98%. 3' truncation point suspiciously on Bam site in A2; end of sequence is an altered RI site.
- TSD not identified.
- Falls in DA2 lineage.
Musmht
- From Musmhthy19, M26156, g199645
- Mouse MHC momclassical class I Thy19.4 gene (H-2 d haplotype)
- 1..330 matches L1MdA2 5501..5830, 98%. 5' cut off; 3' truncated.
- Falls in TF lineage.
Muspr
- From MUSPRPC2, M23236, J03891, g200535
- Mus musculus (strain CD-1) proline rich protein (M14) gene, complete cds, clones MC(14,16,22).
- Compl. of 1776..3764 matches L1MdA2 7362..5375 96%.
- TSD identified: AA(A/G)AAAGACA @ 1757/3762
- Falls in DA2 lineage.
Musrsb5
- From MUSRSBAM5, J00663, g200837
- Mouse repetitive DNA from bamhi digestion, bam5 fragment.
- Fanning, T G. Characterization of a hihly repetitive family of DNA sequences in the mouse. Nucleic Acids Res. 10. 5003-5013 (1982)
- 1..507 matches L1MdA2 6388..6898 93%
- Falls in Z_lineage.
Musrsl1r
- From MUSRSL1R, J02793, g200844
- Mouse R and L1 (3' end ) repetitive elements.
- Tolberg, M E, et al. Structural organization and DNA methylation patterning within the mouse L1 family. J Biol Chem 262, 11167-11175.
- 1..466 matches L1MdA2 6896..7362 89%
- No TSD because 5' end cut off
- Falls in TF lineage.
Mustc (aka Mustc-1)
- From MUSTCRVAD, M94080
- Mouse T-Cell receptor region
- 16,664..17,422 matches L1MdA2 6603..7362 95%
- no obvious TSDs
- Falls just before or around base of Z subfamily
Musu3
- From MUSU3B3A, M23707, g341020
- Mus mjusculus small nuclear RNA (U3B.3) gene. 5' cut off.
- Compl. of 844..1310(end) matches L1MdA2 7362..6893 96% .
- TSD not identified.
- Falls in lineage.
Pg14lh
- from MMPG14LH, X13049
- 4388..5494 match L1MdA2 6257..end; 91%
- 2319..4390 matches L1MdA2 1723..3717; 90%
- Upstream there is a typical AF composite junction to a short F-type promoter monomer, and then a typical junction to a type VI A type promoter.
- TSD = aaatgacaaattt @ 2117/5494
- This is apparently the 3' part of a full length LINE-1 inserted in an actin pseudogene and containing a large internal deletion. It seems reliably to not be a recombinant because it is surrounded by a TSD and the flanks are consistent with a single insertion in an actin pseudogene.
- Ref: Begg, Delius, Leader. 1988. JMB 203:677-687
- Falls in L1Md2 lineage.
- Adey et al., 1991 identify the promoter as a composite AF promoter. Hence the L2 lineage may be all or in part equal to the AF subfamily described in that paper.
PL2
- A L1 cloned from a spretus differential locus after transfer to a C57BL/6J background. The presence of the L1 in the donor C57BL/6J strain (Spret/Ei> is confirmed. See Rikke et al., 1993.
- Sequence covers A2 coordinates 6110..end.
- Sequence unpublished. PL2 sequence
- 5' end cut off past the RI site.
- Falls in the terminal burst of the oMs7024 lineage.
PL3, PL3uf
- An inverted bipartite L1 cloned from a spretus differential locus after transfer to a C57BL/6J background. The presence of the L1 in the donor strain (Spret/Ei) is confirmed. See Rikke et al., 1993.
- PL3uf refers to an unfolded version of the inverted bipartite.
- Sequence is unpublished. PL3uf sequence
- Covers A2 coordinates 6174..7324; extreme 3' end displaced by a premature p(A) tail.
- TSD = GAAATTATCAGAGAA
- Maps to the terminal burst of the oMS475 lineage.
R3
- From MUSIGKVK, K00893, g197462
- Mouse Ig germline kappa v-region flank; R3 repeat
- 358..574 matches L1MdA2 7146..end; inserted in an older L1.
- TSD not identified
- Falls in top of L2 lineage
R4
- From MMDRF3 V01560, L00029, X00153, X00159, g50739
- Mouse dispersed repetitve DNA sequences of the R-family and simple sequence DNA; member of the B2 family of mouse dispersed repetitive DNA sequences.
- Inverted bipartite strs: 5' seg: 84..669 plus strand matches L1MdA2 6807..7362 86% 3' seq: 1..84 neg.str. matches L1MdA2 6086..5973 96%
- TSD not identified.
- Falls in top of L2 lineage.
R8
- 1475..2305 from MDRF3, V01560
- 80% to L1MdA2 6514..end
- May be part of an inverted bipartite structure, but can't be confirmed by TSDs, so only the 3' segment is used.
- There is a second L1 named R4 in this GenBank entry, which is also suspected of being an inverted bipartite.
Ratlin3a
- Full length rat L1 from RATLIN3A, M13100
- TSD identified
- 451..7142 in ratlin3a, including rat-type promoter
- ~85% to L1MdA2 in body
Rattran
- One of the more alignable of the rat sequences to the mouse 3' UTR.
- 1..511 from rattran, M13012

Sequence collections

SPLW31 library from Spret/Ei
- Sequenced clones:
  - SHA - in spretus A2 lineage.
  - SFA - in spretus A2 lineage.
SPLW39 library from Spret/Ei
- Sequenced clones:
  - SAF - L1Md4 lineage above spretus/domesticus split.
DMZLW40 library from M. domesticus strain DMZ.
- PCR-generated library
- 1875 clones arrayed in 96 well plates
- Individual sequences designated with 2 or 3 letter names starting with D
- Sequence covers 6112-7111 (excluding primers).
- PCR recombination/heteroduplex correction measured as affecting < 3% of clones.
PANLW61 library from M. spicilegus strain PANCEVO
- Sequenced clones:
  - PA
  - PD
Clones from Spret/Ei lambda library
- EL2, EL8, EL9, EL10, S1F
- unpublished collection of sequences, Shijun Huang, Liping Wang, this lab.
- EL clones recovered from Spret/Ei by probing with oMS475
- S1F recovered by probing with TF promoter
- EL10 is a partially sequenced full length Ms475 family member with a TF promoter array.
- S1F is a partially sequenced full length Ms7024 family member with a TF promoter array.
- Part of genetic marker project
Naas et al., 1998, DeBerardinis et al., 1998
- Clones were selected for content of full length elements with T_F promoters.
- Sequences cover the entire element except for the extreme ends.
- Members of collection:
  - L1Md-Tf5 - AF081104
  - L1Md-Tf6 - AF081105
  - L1Md-Tf8 - AF081106
  - L1Md-Tf9 - AF081107
  - L1Md-Tf14 - AF081108
  - L1Md-Tf17 - AF081109
  - L1Md-Tf18 - AF081111
  - L1Md-Tf23 - AF081110
  - L1Md-Tf26 - AF081112
  - L1Md-Tf29 - AF081113
  - L1Md-Tf30 - AF081114
- Tf14,18,23,29 have in-frame terminators.
- Not yet included are TF promoters from DeBerardinis & Kazazian (1999):
  - L1Md-Tf2 - AF097473
  - L1Md-Tf16 - AF097474
  - L1Md-Tf19 - AF097475
Casavant and Hardies, 1994
- Cloned RI SacI restriction fragments from spret/Ei
- Selected for position in last 0.4 Myr of tree by hybridization to a probe for 6936C.
- Sequenced region covered is 6621..7152.
- Designated with names SK# or KS#
  - KS101 - AF132342
  - KS105 - AF132343
  - KS106 - AF132344
  - SK1 - AF132345
  - SK11 - AF132346
  - SK13 - AF132347
  - SK2 - AF132348
  - SK20 - AF132349
  - SK23 - AF132351
  - SK3 - AF132352
  - SK30 - AF132353
  - SK31 - AF132354
  - SK4 - AF132355
  - SK5 - AF132356
  - SK6 - AF132357
  - SK7 - AF132358
  - SK9 - AF132359
Casavant and Hardies, 1994a
- Clones from Spret/Ei amplified by PCR between and internal L1 primer and a bubble adapter in the 3' flank.
- Targetted at young elements by use of a PCR primer containing variant 6873 (Ms496).
- Designated with SC#.
- Covering 6874..end. Tendency for 3' truncation suppressed by screening with an extreme 3' end oligo.
- SC6L and R are left and right portions of a clone thought to be a recombinant.
Casavant and Hardies, 1991
- from Spret/Ei, except D13sh1, which was from a Spret/Ei-domesticus hybrid mouse, and then mapped back to the spretus segment.
- PCR amplified from L1 primer to bubble primer in 3' flank.
- Generally recovered 3' truncated clones, apparently due to inefficiency of amplifying across G tract at 3' end.
- Designated SPR#
  - SPR48 6874..7041
  - SPR49 6874..6987
  - SPR68 6874..7085
  - D13sh1 6874..6951
Rikke et al., 1991.
- Cloned Bam5 fragments from M. spretus strain Spret/Ei
- Designated as S#
- Completely sequenced, covering 6391..6891
- Tree in paper correlates with data from Martin et al., 1985 collection.
Martin et al., 1985
- Cloned Bam5 fragments from:
  - M. domesticus Balb/cJ
  - M. caroli
  - M. saxicola (called M. platythrix in the original paper).
- Designated as D#, C#, or P#
- Sequence covered 6391..6683

Nodal and consensus sequences

Ms475node
- Sequence
A2 node 1
- Sequence
Ms7024node
- Sequence
TFnode2
- The parental sequence of the TF family is a recombinant with the 3' end joining the A2 lineage at about 1 Mya, and the 5' end joining the M lineage. See Saxton and Martin, 1998.
- The recombination point is between 3633-3733 in Loeb coodinates.

Last update: 7/8/99.