RetrogeneDB ID: retro_pabe_3052

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:27289781..27291047(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPCPD1
• Ensembl ID: ENSPPYG00000010687
• Aliases: None
• Description: glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26957]

Sequence

>retro_pabe_3052
AGCATGTTATGGAAAGCAACCATTGTACTCAGTGGAGGAGTATAAGTTCAGCATCGCTACTTCAAAGGGTACTTTTTAGA
ACCAAAGACTATCGGTGGTCCATGTCAAGTGATAGTTCACAAGTGGGAGATTCATCTACAACCACGATCAATAACCCCGT
CAGAAAGCGAAATTGTTATTGACGATGGACAATTTGGAATCCACAGTGGTGTTGAAACTCTGGATTCTGGATGGTTGGCA
TGTCAGATTGAAACAAGATTACGTTTGCATTGTTCTGAAAAACCTCCTGTGCCAATAACCAAGAAAAAAATTTAAAAATC
TAGATTTAGGGTGAAGCTGACACTAGAGGGCCTGGAGGAAGATGACGATGATAGGGTATCTCCCACTGTACTTCACAAAA
TATCCAATAGCATGGAGATCTCCTTAATAAGTGACAATGAGTTCAAGTGCAGGCATTCACAGCTGGAGTGTGGTTATGGC
TTACAGTCTGATCATTGGACAGAGTACAGCATACGGACAATGGGACCAGATAACCTGGAACTAATCTTTGATTTTTTTGA
AGAAAATCTCAGTGAGCATGTAGTTCAAGGTGATGCTCTCCATGGACGTGTGGATACAGCTTGTCTCTTATCATCCACCC
TTGCTGAGAGTGGAAAGAGTGCTGGAATTCTTACTCTTCCCATCATAAGCAGAAATTCCAGGAAAACAATAGGCAAAGTG
AGAGTTGACTATATAATTATTAAGCCATTGCCAGGATACAGTTGTGACATGAAATCTTCATTTTCCAAGTATTGGAAGCC
AAGAATACCATTGGATGTTGGCCATCGAGGTGCAGGAAACGCTACAACTACCCAGCTGGCTAAGGAAAATACTATTGCTT
CTTTAAGAAATGCTGATAGTCATGGTGCAGCCTTTGTAGAATTTGATGTACACCTTTCAAAGGAATTTGTGCCCGTGGTA
TATTATGATCTTACCTGTTGTTTGACTATGAAAAAGAAATTTGATCCTGATCCAGTTGAATTATTTGAAATTCCAGTAAA
AAAATTAACATTTGACCATCTCCAGTTGTTAAAGCTCACTCATGTGACTGCACTGAAATCTAAGGATCGGAAATAATCTG
TGGTCCAGGAGGAAAATTCCTTTTCAGAAAATCAGCCATTTCCTTCTGGTAAGATGGTTTTAGAGTGTTTGCCAGAAGAT
GTAGGGTTTAACAGTGAAATAAAATGGATCTGCCAACAAAGGGATGGAATGTGGAATGGTAACATA

Alignment

ORF - retro_pabe_3052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.41 %
• Parental protein coverage: 63.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SMLWKATIVLSRGVSVQYRYFKGYFLEPKTFGGPCQVIVHKWETHLQPRSITPLESEIIIDDGQFGIHNG
          SMLWKATIVLS.GV.VQ.RYFKGYFLEPKT.GGPCQVIVHKWE.HLQPRSITP.ESEI.IDDGQFGIH.G
Retrocopy SMLWKATIVLSGGV*VQHRYFKGYFLEPKTIGGPCQVIVHKWEIHLQPRSITPSESEIVIDDGQFGIHSG

Parental  VETLDSGWLTCQTEIRLRLHYSEKPPVSITKKKLKKSRFRVKLTLEGLEEDDDDRVSPTVLHKMSNSLEI
          VETLDSGWL.CQ.E.RLRLH.SEKPPV.ITKKK..KSRFRVKLTLEGLEEDDDDRVSPTVLHK.SNS.EI
Retrocopy VETLDSGWLACQIETRLRLHCSEKPPVPITKKKI*KSRFRVKLTLEGLEEDDDDRVSPTVLHKISNSMEI

Parental  SLISDNEFKCRHSQPECGYGLQPDRWTEYSIQTMEPDNLELIFDFFEEDLSEHVVQGDALPGHVGTACLL
          SLISDNEFKCRHSQ.ECGYGLQ.D.WTEYSI.TM.PDNLELIFDFFEE.LSEHVVQGDAL.G.V.TACLL
Retrocopy SLISDNEFKCRHSQLECGYGLQSDHWTEYSIRTMGPDNLELIFDFFEENLSEHVVQGDALHGRVDTACLL

Parental  SSTIAESGKSAGILTLPIMSRNSRKTIGKVRVDYIIIKPLPGYSCGMKSSFSKYWKPRIPLDVGHRGAGN
          SST.AESGKSAGILTLPI.SRNSRKTIGKVRVDYIIIKPLPGYSC.MKSSFSKYWKPRIPLDVGHRGAGN
Retrocopy SSTLAESGKSAGILTLPIISRNSRKTIGKVRVDYIIIKPLPGYSCDMKSSFSKYWKPRIPLDVGHRGAGN

Parental  STTTAQLAKVQENTIASLRNAASHGAAFVEFDVHLSKDFVPVVYHDLTCCLTMKKKFDADPVELFEIPVK
          .TTT.QLAK..ENTIASLRNA.SHGAAFVEFDVHLSK.FVPVVY.DLTCCLTMKKKFD.DPVELFEIPVK
Retrocopy ATTT-QLAK--ENTIASLRNADSHGAAFVEFDVHLSKEFVPVVYYDLTCCLTMKKKFDPDPVELFEIPVK

Parental  ELTFDQLQLLKLTHVTALKSKDRKESVVQEENSFSENQPFPSLKMVLESLPEDVGFNIEIKWICQQRDGM
          .LTFD.LQLLKLTHVTALKSKDRK.SVVQEENSFSENQPFPS.KMVLE.LPEDVGFN.EIKWICQQRDGM
Retrocopy KLTFDHLQLLKLTHVTALKSKDRK*SVVQEENSFSENQPFPSGKMVLECLPEDVGFNSEIKWICQQRDGM

Parental  WDGNL
          W.GN.
Retrocopy WNGNI

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	0.11 RPM	70.61 RPM
SRP007412_cerebellum	0.24 RPM	103.60 RPM
SRP007412_heart	0.03 RPM	46.57 RPM
SRP007412_kidney	0.00 RPM	45.94 RPM
SRP007412_liver	0.00 RPM	43.09 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3052 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3052 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3052 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,