RetrogeneDB ID: retro_pabe_767

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:67577850..67579291(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DOK1
• Ensembl ID: ENSPPYG00000012264
• Aliases: None
• Description: docking protein 1, 62kDa (downstream of tyrosine kinase 1) [Source:HGNC Symbol;Acc:2990]

Sequence

>retro_pabe_767
ATGGATGGAGCTGTGATGGAAGGGCCACTCTTTTCGCAGAGTCAGCACTTTGGGACCAAGAGGTGGAGGAAGACATGGGC
CATGCTCTACCCGGCCAGTCCCCATGGCGCAGCGCAGCTTGAGTTCTTTGACCATAAGGGGTCAAGCTCTGGGAGTGGCC
GAGGGAGCTTGTGCCGCCTGGACTGCAAGGTGATCCATCTGGCGAAGTGTGTGAGTTTGGCTCCCGTGGCCGTGGAGAGC
CTCCCTGAGCCCAGCGCCACTGCCTTCCGCCTGGACACTGCACAGCACTAGCACCTGCTGACTGTTGATGTGCCGTCCAG
TGCAGCCTGGTTGCAGACGCTGTGCCAAAACCCCTTTTGGAAAGGCAGCTGGACTCTGGAACCTACCAATAACCCACCTG
AGCTTTCTGCCCTGGAGATGCTGGAGAACTCCTTGTGCAGCCCCACCTGGGAAGGATCCCAGTTCTGGGTAACGGTGCAG
AGGACTGAGGCGGTCGAGCACTGTGGCCTGCATGCCTCCTATGTGCTGAGGGTAGAGGCTGAAAGGCTGACTCTCCTGAC
CATGGGAGCCCAGAGTCAGGTACTGGAGCTGCTCCTGTCCTGGCCCTACACTCTGTTGCATCGCTATGGCCGGGACAAGG
TCATGTTCTCTTTTGAGGCCAGCGCCGCTGCCTCTTGGGCCCTGGAAACTTCACTTACCAGACAGCACAGGGAAATGACA
TCTTCCAGGCAGGTGAGACTGCCATCCATCGGCAGAAGGCCCAGGGAAAGGCCAGACAGGGGCACAATGTTCTCAGAGCT
GATTCCCATGAAAGGAAGATGGCAGAGGGGAAGCTCTCTTCCCCACCTGGCCCCCAAGAGCTCCTTGACAGCCCCCCAGC
CCTGTATGCTGAGCCCTTAGACTCCCTATACATTGCTTCAGGCCCATCCCAGGGCTCCCTGTACTCAGACCTCTTGGACG
GCACCCTTGCTCGGGCAGGAGAGGGAGTACAATGGAAGAAACCTCTCTGTTGGGACTTGTATGAGCATGAGCAGCAGCAG
TTGCTGAAGGCCGGGCTGACGGACCCCAAAGAGGATCCCATCTATGATGAACCCGAGGGCCTGGCCCCAGCCCTTCCCCA
GGGCCTTTATGATCTGCCTTAGGAGCCCAAAGATGCATGGGATGTCAAGCTCAGGTGAAGTAGGAGGGCTACAAGCTCCC
CTACAACCCTGCCACTGATGACCATGCTGTGCCACCCACCCAGAGAACAAAGACCCTCCCTGCTTCCAAGTCCCAGGGCC
CAGCCTTCCCTGAACCTAGTACTGCAACTGGCAGGAGCAGCAAAAGCCACAACTCAGCCCTGTACAGCCAGGTCCAGAAG
AGGGGGGCCTCAGGGAGCTGGGACTGTGTGCTTTCTACAGTAGGGACTGACAGGACTGGGGTCAAGTCAGAGGTCTCTAC
C

Alignment

ORF - retro_pabe_767 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDGAVMEGPLFLQSQRFGTKRWRKTWAVLYPASPHGVARLEFFDHKGSSSGGGRGSSRRLDCKVIRLAEC
          MDGAVMEGPLF.QSQ.FGTKRWRKTWA.LYPASPHG.A.LEFFDHKGSSSG.GRGS..RLDCKVI.LA.C
Retrocopy MDGAVMEGPLFSQSQHFGTKRWRKTWAMLYPASPHGAAQLEFFDHKGSSSGSGRGSLCRLDCKVIHLAKC

Parental  VSVAPVTVETPPEPGATAFRLDTAQRSHLLAADAPSSAAWVQTLCRNAFPKGSWTLASTDNPPKLSALEM
          VS.APV.VE..PEP.ATAFRLDTAQ..HLL..D.PSSAAW.QTLC.N.F.KGSWTL..T.NPP.LSALEM
Retrocopy VSLAPVAVESLPEPSATAFRLDTAQH*HLLTVDVPSSAAWLQTLCQNPFWKGSWTLEPTNNPPELSALEM

Parental  LENSLYSPTWEGSQFWVTVQRTEAAERCGLHGSYVLRVEAERLTLLTVGAQSQILEPLLSWPYTLLRRYG
          LENSL.SPTWEGSQFWVTVQRTEA.E.CGLH.SYVLRVEAERLTLLT.GAQSQ.LE.LLSWPYTLL.RYG
Retrocopy LENSLCSPTWEGSQFWVTVQRTEAVEHCGLHASYVLRVEAERLTLLTMGAQSQVLELLLSWPYTLLHRYG

Parental  RDKVMFSFEAG-RRCPSGPGTFTFQTAQGNDIFQAVETAIHRQKAQGKAGQGHDVLRADSHEGEVAEGKL
          RDKVMFSFEA..RRC..GPG.FT.QTAQGNDIFQA.ETAIHRQKAQGKA.QGH.VLRADSHE...AEGKL
Retrocopy RDKVMFSFEAS<RRCLLGPGNFTYQTAQGNDIFQAGETAIHRQKAQGKARQGHNVLRADSHERKMAEGKL

Parental  PSTPGPQELLDSPPALYAEPLDSLRIAPCPSQDSLYSDPLDSTPARAGEGVQRKKPLYWDLYAHAQQQLL
          .S.PGPQELLDSPPALYAEPLDSL.IA..PSQ.SLYSD.LD.T.ARAGEGVQ.KKPL.WDLY.H.QQQLL
Retrocopy SSPPGPQELLDSPPALYAEPLDSLYIASGPSQGSLYSDLLDGTLARAGEGVQWKKPLCWDLYEHEQQQLL

Parental  KAKLTDPKEDPIYDEPEGLAPVPPQSLYDLPREPKDAW-WCQARVKEEGYELPYNPATDDYAVPPPRSTK
          KA.LTDPKEDPIYDEPEGLAP..PQ.LYDLP.EPKDAW..CQA.VK.EGY.LPYNPATDD.AVPP...TK
Retrocopy KAGLTDPKEDPIYDEPEGLAPALPQGLYDLP*EPKDAW<GCQAQVK*EGYKLPYNPATDDHAVPPTQRTK

Parental  PLLAPKPQGPAFPEPGTATGSGIKSHNSALYSQVQKSGASGSWDCGLSRVGTDKTGVKSEGST
          .L.A.K.QGPAFPEP.TATG...KSHNSALYSQVQK.GASGSWDC.LS.VGTD.TGVKSE.ST
Retrocopy TLPASKSQGPAFPEPSTATGRSSKSHNSALYSQVQKRGASGSWDCVLSTVGTDRTGVKSEVST

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	2.65 RPM
SRP007412_cerebellum	0.00 RPM	0.61 RPM
SRP007412_heart	0.00 RPM	1.54 RPM
SRP007412_kidney	0.00 RPM	4.67 RPM
SRP007412_liver	0.00 RPM	3.58 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_767 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_767 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_767 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000115325	1 retrocopy	retro_hsap_891,
Macaca mulatta	ENSMMUG00000002139	1 retrocopy	retro_mmul_1103,
Nomascus leucogenys	ENSNLEG00000001010	1 retrocopy	retro_nleu_391,
Pongo abelii	ENSPPYG00000012264	1 retrocopy	retro_pabe_767 ,
Pan troglodytes	ENSPTRG00000012100	1 retrocopy	retro_ptro_615,