RetrogeneDB ID: retro_mmus_3024

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:42125202..42126221(-)
• Located in intron of: ENSMUSG00000090619

Retrocopy information

• Ensembl ID: ENSMUSG00000092257
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gapdhs
• Ensembl ID: ENSMUSG00000061099
• Aliases: Gapdhs, Gapd-s, Gapds
• Description: glyceraldehyde-3-phosphate dehydrogenase, spermatogenic [Source:MGI Symbol;Acc:MGI:95653]

Sequence

>retro_mmus_3024
CCTCATCCCGTAGACAAAATGGTGAAGGTCGGTGTGAACGGATTTGGCCGTATTGGGCGCCTGGTCACCAGGGCTGCCAT
CTGCAGTGGCAAAGTGGAGATTGTTGCCATCAACGACCCCTTCATTGACCTCAACTACATGGTCTACATGTTCCAGTATG
ATTCCACCCACGGCAAGTTCAACGGCACAGTCAAGGCCGAGAATGGGAAGCTTGTCATCAACGGGAAGCCCATCACCATC
TTCCAGGAGCGAGGCCCCACTAACATCAAATGGGGTGAGGCCGGTGCTGAGTATGTCGTGGAGTCTACTGGTGTCTTCAC
CACCATGGAGAAGGCCAGGGCCCACTTGAAGGGTGGAGCCAAAAGTGTCATCATCTCTGCCCCTTCTGCCGATGCCCCCA
TGTTTGTGATGGGTGTGAACCACGAGAAATATGACAACTCACTCAAGATTGTCAGCAATGCATCCTGCACCACCAACTGC
TTAGCCCCCCTGGCCAAGGTCATCCATGACAACTTTGGCATTGTGGAAGGGCTCATGACCACGGTCCATGCCATCACTGC
CACCCAGAAGACTGTGGATGGCCCCTCTGGAAAGCTGTGGCATGATGGCCGTGGGGCTGCCCAGAACATCATCCCTGCAT
CCACACTGGTGCTGCCAAGGCTGTGGGCAAGGTCATCTCAGAGCTGAACGGGAAGCTCACTGGCATGGCCTTCTGTGTTC
CTACCCCCAATGTGTCCGTCGTGGATCTGACGTGCCGCCTGGAGAAACCTGCCAAGTATGATGACATCAAGAAGGTGGTG
AAGCAGGCATCTGAGGGCCCACTGAAGGGCATCATGGGCTACACTGAGGACCAGGTTGTCTCCTGCGACTTCAACAGCAA
CTCCCACTCTTCCACCTTCGATGTCGGGGCTGGCATTGCTCTCAATGACAACTTTGTCAAGCTCATTTCCTGGTATGACA
ATGAATATGGCTACAGCAACAGGGTGGTGGACCTCATGGCCTACATGGCCTCCAAGGAG

Alignment

ORF - retro_mmus_3024 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.22 %
• Parental protein coverage: 78.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPPLQKPARELTVGINGFGRIGRLVLRVCMEKG-IRVVAVNDPFIDPEYMVYMFKYDSTHGRYKGNVEHK
          P.P..K......VG.NGFGRIGRLV.R.....G....VA.NDPFID..YMVYMF.YDSTHG...G.V...
Retrocopy PHPVDKMVK---VGVNGFGRIGRLVTRAAICSGKVEIVAINDPFIDLNYMVYMFQYDSTHGKFNGTVKAE

Parental  NGQLVVDNLEINTYQCKDPKEIPWSSIGNPYVVECTGVYLSIEAASAHISSGARRVVVTAPSPDAPMFVM
          NG.LV.....I...Q...P..I.W...G..YVVE.TGV....E.A.AH...GA..V...APS.DAPMFVM
Retrocopy NGKLVINGKPITIFQERGPTNIKWGEAGAEYVVESTGVFTTMEKARAHLKGGAKSVIISAPSADAPMFVM

Parental  GVNEKDYNPGSMTIVSNASCTTNCLAPLAKVIHENFGIVEGLMTTVHSYTATQKTVDGPSKKDWR-GGRG
          GVN...Y...S..IVSNASCTTNCLAPLAKVIH.NFGIVEGLMTTVH..TATQKTVDGPS.K.W..G...
Retrocopy GVNHEKYD-NSLKIVSNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKTVDGPSGKLWHDGRGA

Parental  AHQNIIPSS-TGAAKAVGKVIPELKGKLTGMAFRVPTPNVSVVDLTCRLAKPASYSAITEAVKAAAKGPL
          A...I..S..TGAAKAVGKVI.EL.GKLTGMAF.VPTPNVSVVDLTCRL.KPA.Y..I...VK.A..GPL
Retrocopy AQNIIPAST<TGAAKAVGKVISELNGKLTGMAFCVPTPNVSVVDLTCRLEKPAKYDDIKKVVKQASEGPL

Parental  AGILAYTEDQVVSTDFNGNPHSSIFDAKAGIALNDNFVKLVAWYDNEYGYSNRVVDLLRYMFSRE
          .GI..YTEDQVVS.DFN.N.HSS.FD..AGIALNDNFVKL..WYDNEYGYSNRVVDL..YM.S.E
Retrocopy KGIMGYTEDQVVSCDFNSNSHSSTFDVGAGIALNDNFVKLISWYDNEYGYSNRVVDLMAYMASKE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.58 RPM	1.78 RPM
SRP007412_cerebellum	0.13 RPM	3.82 RPM
SRP007412_heart	1.25 RPM	0.84 RPM
SRP007412_kidney	0.58 RPM	1.14 RPM
SRP007412_liver	0.55 RPM	0.74 RPM
SRP007412_testis	0.05 RPM	1121.93 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3024 was not detected

EST

No EST(s) were mapped for retro_mmus_3024 retrocopy.

TSS

No TSS is located nearby retro_mmus_3024 retrocopy 5' end.

Lab

retro_mmus_3024 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3024 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 154 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000057666	109 retrocopies	retro_mmus_1029, retro_mmus_1082, retro_mmus_1136, retro_mmus_1193, retro_mmus_1249, retro_mmus_1319, retro_mmus_1328, retro_mmus_136, retro_mmus_1365, retro_mmus_1371, retro_mmus_1467, retro_mmus_1474, retro_mmus_1480, retro_mmus_1615, retro_mmus_1692, retro_mmus_1721, retro_mmus_1728, retro_mmus_1886, retro_mmus_1922, retro_mmus_1957, retro_mmus_1983, retro_mmus_1985, retro_mmus_2009, retro_mmus_2020, retro_mmus_2030, retro_mmus_2100, retro_mmus_211, retro_mmus_2119, retro_mmus_2122, retro_mmus_2148, retro_mmus_2158, retro_mmus_2175, retro_mmus_2206, retro_mmus_2216, retro_mmus_2248, retro_mmus_2298, retro_mmus_2370, retro_mmus_2371, retro_mmus_2389, retro_mmus_2463, retro_mmus_2477, retro_mmus_2481, retro_mmus_2512, retro_mmus_2556, retro_mmus_2587, retro_mmus_2623, retro_mmus_2626, retro_mmus_2647, retro_mmus_2681, retro_mmus_2755, retro_mmus_2761, retro_mmus_2764, retro_mmus_2848, retro_mmus_2872, retro_mmus_2911, retro_mmus_2912, retro_mmus_2913, retro_mmus_2914, retro_mmus_2915, retro_mmus_2920, retro_mmus_2932, retro_mmus_2943, retro_mmus_300, retro_mmus_3036, retro_mmus_3064, retro_mmus_3120, retro_mmus_3137, retro_mmus_3140, retro_mmus_3148, retro_mmus_3151, retro_mmus_3188, retro_mmus_3193, retro_mmus_3197, retro_mmus_3216, retro_mmus_3228, retro_mmus_3306, retro_mmus_3335, retro_mmus_3336, retro_mmus_3357, retro_mmus_3377, retro_mmus_3445, retro_mmus_3514, retro_mmus_3575, retro_mmus_3650, retro_mmus_3658, retro_mmus_3693, retro_mmus_3716, retro_mmus_3814, retro_mmus_416, retro_mmus_437, retro_mmus_48, retro_mmus_553, retro_mmus_608, retro_mmus_619, retro_mmus_628, retro_mmus_635, retro_mmus_698, retro_mmus_745, retro_mmus_765, retro_mmus_766, retro_mmus_787, retro_mmus_811, retro_mmus_893, retro_mmus_914, retro_mmus_921, retro_mmus_946, retro_mmus_952, retro_mmus_976, retro_mmus_996,
Mus musculus	ENSMUSG00000061099	2 retrocopies	retro_mmus_3024 , retro_mmus_528,
Otolemur garnettii	ENSOGAG00000009491	25 retrocopies	retro_ogar_1269, retro_ogar_1332, retro_ogar_1460, retro_ogar_1472, retro_ogar_1798, retro_ogar_1968, retro_ogar_2074, retro_ogar_2266, retro_ogar_2376, retro_ogar_2446, retro_ogar_2469, retro_ogar_2631, retro_ogar_2647, retro_ogar_2884, retro_ogar_2957, retro_ogar_315, retro_ogar_3197, retro_ogar_3262, retro_ogar_3517, retro_ogar_355, retro_ogar_468, retro_ogar_582, retro_ogar_632, retro_ogar_658, retro_ogar_785,
Petromyzon marinus	ENSPMAG00000009321	1 retrocopy	retro_pmar_9,
Pan troglodytes	ENSPTRG00000010848	1 retrocopy	retro_ptro_2211,
Tupaia belangeri	ENSTBEG00000008617	16 retrocopies	retro_tbel_1017, retro_tbel_1193, retro_tbel_124, retro_tbel_1650, retro_tbel_1685, retro_tbel_2010, retro_tbel_2486, retro_tbel_249, retro_tbel_2793, retro_tbel_2832, retro_tbel_2873, retro_tbel_2929, retro_tbel_3117, retro_tbel_425, retro_tbel_4292, retro_tbel_4346,