RetrogeneDB ID: retro_ptro_2625

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:55654286..55655806(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: GPCPD1
• Ensembl ID: ENSPTRG00000013228
• Aliases: None
• Description: None

Sequence

>retro_ptro_2625
AGCATGTTATGGAAAGCAACCATTTTACTCAGTAGAGGAGTATCAGTTCAGCATTGCTACTTCAAAGGGTACTTTTTAGA
ACCAAAGACTATCGGTGGTCCATGTCAAGTGATAGTTCACAAGTGGGAGATTCATCTACAACCACGATCAATAACCCCGT
CAGAAAGTGAAATTGTTATTGACCATGGACAATTTGGAATCCACAGTGGTGTTGAAACTCTGGATTCTGCATGGCTGGCA
TGTCAGACTGAAATAAGATTACGTTTGCATTATTCTGAAAAACCTCCTGTGTCAATAACCAAGAAAAAAATTTAAAAATC
TAGATTTAGGGTGAAGCTGACACTAGAGGGCCTGGAGGAAGATGACGATGATAGGGTATCTCCCACTGTACTTCACAAAA
TGTCCAATAGCATGGAGATATCCTTAATATGTGACAATGAGTTCCAGTGCAGGCATTCACAGCTGGAGTGTGGTTATGGC
TTACAGTCTGATCGTTGGACAGAGTACAGCATACAGACAATGGGACCAGATAACCTGGAACTAATCTTTGATTTTTTTGA
AGAAGATCTCAGTGAGCACATAGTTCAAGGTGATGCCCTCCCTGGACGTGTGGGTACAGCTTGTCTCTTATTATCCACCA
TTGCTGAGAGTGGAAAGAGTGCTGGAATTCTTACTCTTCCCTACATGAGCAGAAATTCCAGGAAAACAATAGGCAAAGTG
AGAGTCGACTATATAATTATTAAGCCATTGCCAGGATACAGTTGTGACATGAAATCTTCATTTTCCAGTATTGGAAGCCA
AGAATACCACTGGATGTTGGCCATCGAGGTGTGGGAAACACTACAACTGCCCAGCTGGCTAAAGAAAATACTATTGCTTC
TTTAAGAAATGCTGCTAGTCACAGTGCAGCCTTTGTAGAATTTGATGTACACCTTTCAAAGGACTTTGTGCCCATGGTAT
ATCATGATCTTACCTGTTGTTTGACTATGAAAAAGAAATTTGATGCTGATCCACTTGAATTATTTGAAATTCCAGTAAAA
AAAATTAACATTTGACCATCTCCAGTTGTTAAAGCTCACTCATGTGACTGCACTGAAATCTAAGGATTGGAAACAATCTG
TGGTCCAGGAGGAAAATTCCTTTTCAGAAAATCAGGCATTTCCTTCTCGTAAGATGGTTTTAGAGTGTTTGCCAGAAGAT
GTAGGGTTTAACATTGAAATAAAATGGATCTGCCAGCAAAGGGATGGAATGTGGGATGGTAACTTATCAACATATTTTGG
CATGAATCTGTTTTTGGATATAACTTTAAAAACTGTTTTAGAAAATTCTGGGAAGAGAGAATAGTGTTTTCTTCATTTGA
TGCAGATATTTGCACAATGGTTTGGCAAAAGCAGAACAAATATCCCATATTATTTTTAACTGAAGGAAAATCTGAGATTT
ATCCTGAACTCATGGACCTCAGATCTCCGACAACCCCCATTGCAATGAGCTTTGCACAGTTTGAAAATCTACTAGGGATA

Alignment

ORF - retro_ptro_2625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.64 %
• Parental protein coverage: 75.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SMLWKATIVLSRGASVQYRYFKGYFLEPKTIGGPCQVIVHKWETHLQPRSITPLESEIIIDDGQFGIHNG
          SMLWKATI.LSRG.SVQ..YFKGYFLEPKTIGGPCQVIVHKWE.HLQPRSITP.ESEI.ID.GQFGIH.G
Retrocopy SMLWKATILLSRGVSVQHCYFKGYFLEPKTIGGPCQVIVHKWEIHLQPRSITPSESEIVIDHGQFGIHSG

Parental  VETLDSGWLTCQTEIRLRLHYSEKPPVSITKKKLKKSRFRVKLTLEGLEEDDDDRVSPTVLHKMSNSLEI
          VETLDS.WL.CQTEIRLRLHYSEKPPVSITKKK..KSRFRVKLTLEGLEEDDDDRVSPTVLHKMSNS.EI
Retrocopy VETLDSAWLACQTEIRLRLHYSEKPPVSITKKKI*KSRFRVKLTLEGLEEDDDDRVSPTVLHKMSNSMEI

Parental  SLISDNEFKCRHSQPECGYGLQPDRWTEYSIQTMEPDNLELIFDFFEEDLSEHVVQGDALPGHVGTACLL
          SLI.DNEF.CRHSQ.ECGYGLQ.DRWTEYSIQTM.PDNLELIFDFFEEDLSEH.VQGDALPG.VGTACLL
Retrocopy SLICDNEFQCRHSQLECGYGLQSDRWTEYSIQTMGPDNLELIFDFFEEDLSEHIVQGDALPGRVGTACLL

Parental  SSTIAESGKSAGILTLPIMSRNSRKTIGKVRVDYIIIKPLPGYSCDMKSSFS-KYWKPRIPLDVGHRGAG
          .STIAESGKSAGILTLP.MSRNSRKTIGKVRVDYIIIKPLPGYSCDMKSSFS..YWKPRIPLDVGHRG.G
Retrocopy LSTIAESGKSAGILTLPYMSRNSRKTIGKVRVDYIIIKPLPGYSCDMKSSFS<QYWKPRIPLDVGHRGVG

Parental  NSTTTAQLAKVQENTIASLRNAASHGAAFVEFDVHLSKDFVPVVYHDLTCCLTMKKKFDADPVELFEIP-
          N.TTTAQLAK..ENTIASLRNAASH.AAFVEFDVHLSKDFVP.VYHDLTCCLTMKKKFDADP.ELFEIP.
Retrocopy N-TTTAQLAK--ENTIASLRNAASHSAAFVEFDVHLSKDFVPMVYHDLTCCLTMKKKFDADPLELFEIP>

Parental  VKELTFDQLQLLKLTHVTALKSKDRKESVVQEENSFSENQPFPSLKMVLESLPEDVGFNIEIKWICQQRD
          ...LTFD.LQLLKLTHVTALKSKD.K.SVVQEENSFSENQ.FPS.KMVLE.LPEDVGFNIEIKWICQQRD
Retrocopy XXXLTFDHLQLLKLTHVTALKSKDWKQSVVQEENSFSENQAFPSRKMVLECLPEDVGFNIEIKWICQQRD

Parental  GMWDGNLSTYFDMNLFLDIILKTVLENSGKR-RIVFSSFDADICTMVRQKQNKYPILFLTQGKSEIYPEL
          GMWDGNLSTYF.MNLFLDI.LKTVLENSGKR.RIVFSSFDADICTMV.QKQNKYPILFLT.GKSEIYPEL
Retrocopy GMWDGNLSTYFGMNLFLDITLKTVLENSGKR<RIVFSSFDADICTMVWQKQNKYPILFLTEGKSEIYPEL

Parental  MDLRSRTTPIAMSFAQFENLLGI
          MDLRS.TTPIAMSFAQFENLLGI
Retrocopy MDLRSPTTPIAMSFAQFENLLGI

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_prefrontal_cortex	0.02 RPM	82.94 RPM
SRP007412_cerebellum	0.00 RPM	141.35 RPM
SRP007412_heart	0.00 RPM	26.90 RPM
SRP007412_kidney	0.00 RPM	23.35 RPM
SRP007412_liver	0.00 RPM	10.93 RPM
SRP007412_testis	0.11 RPM	44.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2625 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2625 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2625 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000125772	1 retrocopy	retro_hsap_3854,
Pongo abelii	ENSPPYG00000010687	1 retrocopy	retro_pabe_3052,
Pan troglodytes	ENSPTRG00000013228	1 retrocopy	retro_ptro_2625 ,
Ictidomys tridecemlineatus	ENSSTOG00000006827	1 retrocopy	retro_itri_1811,