RetrogeneDB ID: retro_mmus_2552

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:24647683..24648733(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000038165
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gpd1l
• Ensembl ID: ENSMUSG00000050627
• Aliases: Gpd1l, 2210409H23Rik, D9Ertd660e
• Description: glycerol-3-phosphate dehydrogenase 1-like [Source:MGI Symbol;Acc:MGI:1289257]

Sequence

>retro_mmus_2552
GTGGTGGCTGAGCCTCTGAAGGTGAGCATCGTGGGCTCAGGGAACTGGGCGTCAGCTGTTTCAAAAATCATTGGGAACAA
TGTGAAGACCCTGAAGAAGTTTGCTTCCCCGGTCAAGATGTGGGTATTTGAAGAAATGGTCGATGGGAGGAAGCTGACGG
ACATCATCAACCGTGACCATGAAAACATAAAGTACCTGCCTGGACACAGGCTGCCCGAGAACGTGATGGCCACCCCAAGT
CTCAGCCAGGCTGTGCAGGATGCAGATCTTCTGGTGTTTGCTTTCCCACACCAGTTCATTCGAACCGTCTGTGATGAGAT
TGCTGAGGTAGTGCCCAGGAAGGCCCGGGGCCTCACCCTCATCAAGGGCATAGACGAGAACCCTGAGAGCCTGAAACTTA
TCTCTGACATCATCCGGGAAAAAGTGAACATAGACGTCAGCGTGCTGATGGGGGCCAACTTAGCCAACGAGGTGGCCGCA
GAGTTCTTCTGTGAGACCACCATTGGCAGCAAGGTGCTGCAGAATGGCCTTCTCTTCAAAGAGCTTTTTCAGACCCCTAA
CTTCCAAGTCACTGTGGTAGAAGATTCAGACACAGTGGAGCTGTGCGGGGCTCTAAAGAACATTGTGGCCATGGGGGCCG
GCTTTTGTGACAGCTTCTGTAGTGGAGACAGCACCAAGGCTGCTGTCATCCGCCTGGGCCTCATGGAGATGATTGCTTTT
GCCAGGATTTTCTCCAAGGGTCAGGTGTCCATAGCCACTTTCCTGGAGAGCTGTGGGGTGGCCGACCTCGTTACTACCTG
CTATGGGGGGCGGAACCGAAAGGTAGCGGAAGCCTTCGCCAGGACAGGAAAAAGTATTGAGGAGTTGGAGAAGGAGATGC
TGAAGGGACAGAAGCTGCAAGGGCCACACACCTCTGCCCAGGTGTACCGCATCCTCAAGCAGAAGGGGCTGCTAGACGAG
TTTCCCTTGTTCACAGTTGTGTATCAAATCTGTCACGAGGGCAGACCAGTTGCAGAGCTGATACCGTGTCTACAGAACCA
CCCAGAGTAC

Alignment

ORF - retro_mmus_2552 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.43 %
• Parental protein coverage: 99.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAPLKVCIVGSGNWGSAVAKIIGSNVKTLQKFSSTVKMWVFEETVNGRKLTDIINNDHENVKYLPGHK
          ..A.PLKV.IVGSGNW.SAV.KIIG.NVKTL.KF.S.VKMWVFEE.V.GRKLTDIIN.DHEN.KYLPGH.
Retrocopy VVAEPLKVSIVGSGNWASAVSKIIGNNVKTLKKFASPVKMWVFEEMVDGRKLTDIINRDHENIKYLPGHR

Parental  LPENVVAVPNLSEAVQDADLLVFVIPHQFIHKICDEITGRVPEKALGITLIKGIDEGPDGLKLISDIIRE
          LPENV.A.P.LS.AVQDADLLVF..PHQFI...CDEI...VP.KA.G.TLIKGIDE.P..LKLISDIIRE
Retrocopy LPENVMATPSLSQAVQDADLLVFAFPHQFIRTVCDEIAEVVPRKARGLTLIKGIDENPESLKLISDIIRE

Parental  KMGIDISVLMGANIASEVAAEKFCETTIGSKVMQNGLLFKELLQTPNFRITVVDDADTVELCGALKNIVA
          K..ID.SVLMGAN.A.EVAAE.FCETTIGSKV.QNGLLFKEL.QTPNF..TVV.D.DTVELCGALKNIVA
Retrocopy KVNIDVSVLMGANLANEVAAEFFCETTIGSKVLQNGLLFKELFQTPNFQVTVVEDSDTVELCGALKNIVA

Parental  VGAGFCDGLRCGDNTKAAVIRLGLMEMIAFAKIFCKGQVSTATFLESCGVADLITTCYGGRNRRVAEAFA
          .GAGFCD....GD.TKAAVIRLGLMEMIAFA.IF.KGQVS.ATFLESCGVADL.TTCYGGRNR.VAEAFA
Retrocopy MGAGFCDSFCSGDSTKAAVIRLGLMEMIAFARIFSKGQVSIATFLESCGVADLVTTCYGGRNRKVAEAFA

Parental  RTGKTIEELEKELLNGQKLQGPQTSAEVYRILRQKGLLDKFPLFTAVYQICYEGRPVTQMLSCLQSHPEH
          RTGK.IEELEKE.L.GQKLQGP.TSA.VYRIL.QKGLLD.FPLFT.VYQIC.EGRPV.....CLQ.HPE.
Retrocopy RTGKSIEELEKEMLKGQKLQGPHTSAQVYRILKQKGLLDEFPLFTVVYQICHEGRPVAELIPCLQNHPEY

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	0.00 RPM	107.73 RPM
SRP007412_cerebellum	0.00 RPM	64.83 RPM
SRP007412_heart	0.00 RPM	63.60 RPM
SRP007412_kidney	0.00 RPM	57.88 RPM
SRP007412_liver	0.00 RPM	34.68 RPM
SRP007412_testis	118.05 RPM	6.54 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2552 was not detected

EST

No EST(s) were mapped for retro_mmus_2552 retrocopy.

TSS

No TSS is located nearby retro_mmus_2552 retrocopy 5' end.

Lab

retro_mmus_2552 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2552 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2035

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009826	1 retrocopy	retro_btau_1671,
Choloepus hoffmanni	ENSCHOG00000012633	5 retrocopies	retro_chof_1033, retro_chof_306, retro_chof_340, retro_chof_620, retro_chof_724,
Loxodonta africana	ENSLAFG00000013996	1 retrocopy	retro_lafr_101,
Microcebus murinus	ENSMICG00000011060	1 retrocopy	retro_mmur_1205,
Mus musculus	ENSMUSG00000050627	3 retrocopies	retro_mmus_1348, retro_mmus_2552 , retro_mmus_3695,
Oryctolagus cuniculus	ENSOCUG00000010093	2 retrocopies	retro_ocun_1529, retro_ocun_1588,
Otolemur garnettii	ENSOGAG00000013243	1 retrocopy	retro_ogar_285,
Procavia capensis	ENSPCAG00000016132	1 retrocopy	retro_pcap_316,
Rattus norvegicus	ENSRNOG00000026455	2 retrocopies	retro_rnor_2035, retro_rnor_2474,
Sus scrofa	ENSSSCG00000021977	1 retrocopy	retro_sscr_154,