RetrogeneDB ID: retro_pabe_3541

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:14568585..14569305(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020018
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DUSP8
• Ensembl ID: ENSPPYG00000002903
• Aliases: None
• Description: dual specificity phosphatase 8 [Source:HGNC Symbol;Acc:3074]

Sequence

>retro_pabe_3541
GATCTGATGACGCAGATTGGAATAAGCTACTGTCCTCAATGCCAGCAACTCCTGCCCCAAGCCTGACTTCATCTACCAGA
GCCGCTTCATGCGGGTCCCCATCAACGACAACTACTGTGAAAAGCTGCTGTCCTGGCTGGACAAGTCCATCGAGTTCGTC
GATAAAACCAAGCTGTCCAGCTGCCAAGTCATCGTCCACTGTCTGGCCGGCATCTCCTGCTGTGCCACCATTGCCATCAC
CTACATCATGAAGACCATGGGCATGTCCTCCGAAGACGCCTACAGGTTTGTGAAGGACCAGCACCCGTCCATCTCGCCCA
ACTTCAACTTCCTGGGCCAGCTGCTGGAGTATGAGCGCAGCCTGAAGCTGTTGGCCGCCGTGCAGGGCGACGCGAGCACC
CCCTTAGGGACGCCGGAGCCTCCCCCCAGCCCTGCGGCCGGGACCCCGCTGCCATGGCTGCCACCACCTACCTCAGAGAG
CGCTGCCACCAGGAGTGCAGCTGCCAGGGAGGGCGGCCCGAGCGCAGGCGTGGAGCCCCCCGCGCCCCCCACGGCCACCA
GCACGCTGCAGCAGGGCCTGCGCAGCCTGCACCTCTCTGACTGCCTGCAGGACGCCAGCCGCCTCAAGCCCTTCTTCTCT
CTGGACATCAAGTCGGCCTACGCCCCCAGCCGGCTGCCCGACGGCCCGGGCCCAGCGACCCCGGCGAGGCCCCGAAGCTC

Alignment

ORF - retro_pabe_3541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.9 %
• Parental protein coverage: 64.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLMTQNGISY-VLNASNSCPKPDFICESRFMRVPINDNYCEKLLPWLDKSIEFIDKAKLSSCQVIVHCLA
          DLMTQ.GISY.VLNASNSCPKPDFI..SRFMRVPINDNYCEKLL.WLDKSIEF.DK.KLSSCQVIVHCLA
Retrocopy DLMTQIGISY>VLNASNSCPKPDFIYQSRFMRVPINDNYCEKLLSWLDKSIEFVDKTKLSSCQVIVHCLA

Parental  GISRSATIAIAYIMKTMGMSSDDAYRFVKDRRPSISPNFNFLGQLLEYERSLKLLAALQGDPGTPSGTPE
          GIS..ATIAI.YIMKTMGMSS.DAYRFVKD..PSISPNFNFLGQLLEYERSLKLLAA.QGD..TP.GTPE
Retrocopy GISCCATIAITYIMKTMGMSSEDAYRFVKDQHPSISPNFNFLGQLLEYERSLKLLAAVQGDASTPLGTPE

Parental  PPPSPAAGALLPRLPPPTSESAATGNAAAREGGPSAGGEPPAPPTPPATSALQQGLRGLHLSSDRLQDTN
          PPPSPAAG..LP.LPPPTSESAAT..AAAREGGPSAG.EPPAPPT..ATS.LQQGLR.LHL.SD.LQD..
Retrocopy PPPSPAAGTPLPWLPPPTSESAATRSAAAREGGPSAGVEPPAPPT--ATSTLQQGLRSLHL-SDCLQDAS

Parental  RLKRSFSLDI-SAYAPSRRPDG-PGPPDPGEAPKL
          RLK..FSLDI.SAYAPSR.PDG.PGP.DPGEAPKL
Retrocopy RLKPFFSLDIKSAYAPSRLPDG<PGPSDPGEAPKL

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	0.00 RPM	21.12 RPM
SRP007412_cerebellum	0.00 RPM	15.44 RPM
SRP007412_heart	0.00 RPM	1.66 RPM
SRP007412_kidney	0.00 RPM	1.72 RPM
SRP007412_liver	0.00 RPM	0.86 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3541 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3541 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3541 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000184545	5 retrocopies	retro_hsap_567, retro_hsap_569, retro_hsap_572, retro_hsap_594, retro_hsap_669,
Pongo abelii	ENSPPYG00000002903	2 retrocopies	retro_pabe_3541 , retro_pabe_650,