RetrogeneDB ID: retro_ptro_615

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:69975956..69977397(-)
• Located in intron of: ENSPTRG00000004032

Retrocopy information

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

Parental gene information

• Parental gene symbol: DOK1
• Ensembl ID: ENSPTRG00000012100
• Aliases: None
• Description: None

Sequence

>retro_ptro_615
ATGGACGGAGCTATGACAGAAGGGCCGCTCTTTTCGCAGAGTCAGCACTTTGGGACCAAGAGGTGGAGGAAGACCTGGGC
CATGCTCTACCCGGCCAGTCCCCATGGCATAGCGCGGCTCAAGTTCTTTGACCATAAGGGGTCGAGCTCTGGGAGTGGCC
GAGGGAGCTCGTGCTGCCTGGACTGCAAGGTGATCCATCTGGCGAAGTGTGTGAGTTTGGTCCCCGTGGCCGTGGAGAGC
CTCCCTGAGCCCAGCGCCACTGCCTTCCGCCTGGACACTGCACAGCACTAGCACCTGCTGGCTGTTGATGTGCCGTCCAG
TGCAGCCTGGTTGCAGACGCTGTGCCAAAACCCCCTTCGGAAAGGCAGCTGGACTCTGGAACCTACCAATAACCCACCTG
AGCTTTCTGCCCTGGAGATGCTGGAGAACTCCTTGTGCAGCCCCACCTGGGAAGGATCCCAGTTCTGGGTAACGGTGCAG
AGGACTGAGGCGGTCGAGCACTGTGGCCTGCATGCCTCCTACGTGCTGAGGGTGGAGGCTGAAAGCCTGACTCTCCTGAC
CATGGGAGCCCAGAGTCAGGTACCGGAGCTGCTCCTGTCCTGGCCCTACACTCTGTTGCATTGCTATGGCCGGGACAAGG
TCATGTTCTCTTTTGAGGCCAGCGCCGCTGCCTCTTGGGCCCTGGAACCTTCACTTTCCAGACGGCACAGGGAAATGACA
TCTTCCAGGCAGATGAGACTGCCATCCACCGGCAGAAGGCCCAGGGAAAGGCCAGACAGGGGCACAATGCTCTCAGAGCT
GATTCCTATGAAAGGAAGGTGGTAGAGGGGAAGTTCTCTTCCCCACCTGGCCCCCAAGAGCTCCTTGAAAGCCCCCCAGC
CCTGTATGCTGAGCCCTTAGACTCCCTGCACATTGCTTCAGGCCCATCCCAGGGCTCCCTATACTCAGACCTCTTGGACG
GCACCCTTGCTTGGGCAGGAGAGGGAGTACAATGGAAGAAACCTCTCTATTGGGACTTGTATGAGCATGAGCAGCAGCAG
TTGCTGAAGGCCAAGCTGACGGACCCCAAAGAGGATCCCATCTATGATGAACCCGAGGGCCTGGCCCCAGCCCTTCCCCA
GGGCCTTTATGATCTGCCTTAGGAGCCCAAAGATGTGTGGGATGTCAAGCTCAGGTGAAGTAGGAGGGCTACAAGCTCCC
CTACAACCCTGCCACTGATGACTACGCTATGCCACCCACCCAGAGAACAAAGACCCTCCCTGCTTCCAAGTCCCAGGGCC
CAGCCTTCCCTGAACCTAGTACTGCAACTGGCAGGAGCAGCAAAAGCCACAACTCAGCCCTGTACAGCCAGGTCCAGAAG
AGTGGAGCCTCAGGGAGCTGGGACTGTGTGCTTTCTACAGTAGGGACTGACAGGACTGGGGTCAAGTCAGAGGTCTCTAC
C

Alignment

ORF - retro_ptro_615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.16 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDGAVMEGPLFLQSQRFGTKRWRKTWAVLYPASPHGVARLEFFDHKGSSSGGGRGSSRRLDCKVIRLAEC
          MDGA..EGPLF.QSQ.FGTKRWRKTWA.LYPASPHG.ARL.FFDHKGSSSG.GRGSS..LDCKVI.LA.C
Retrocopy MDGAMTEGPLFSQSQHFGTKRWRKTWAMLYPASPHGIARLKFFDHKGSSSGSGRGSSCCLDCKVIHLAKC

Parental  VSVAPVIVETPPEPGATAFRLDTAQRSHLLAADAPSSAAWVQTLCRNAFPKGSWTLAPTDNPPKLSALEM
          VS..PV.VE..PEP.ATAFRLDTAQ..HLLA.D.PSSAAW.QTLC.N...KGSWTL.PT.NPP.LSALEM
Retrocopy VSLVPVAVESLPEPSATAFRLDTAQH*HLLAVDVPSSAAWLQTLCQNPLRKGSWTLEPTNNPPELSALEM

Parental  LENSLYSPTWEGSQFWVTVQRTEAAERCGLHGSYVLRVEAERLTLLTVGAQSQILEPLLSWPYTLLRRYG
          LENSL.SPTWEGSQFWVTVQRTEA.E.CGLH.SYVLRVEAE.LTLLT.GAQSQ..E.LLSWPYTLL..YG
Retrocopy LENSLCSPTWEGSQFWVTVQRTEAVEHCGLHASYVLRVEAESLTLLTMGAQSQVPELLLSWPYTLLHCYG

Parental  RDKVMFSFEAG-RRCPSGPGTFTFQTAQGNDIFQAVETAIHRQKAQGKAGQGHDVLRADSQEGEVAEGKL
          RDKVMFSFEA..RRC..GPGTFTFQTAQGNDIFQA.ETAIHRQKAQGKA.QGH..LRADS.E..V.EGK.
Retrocopy RDKVMFSFEAS<RRCLLGPGTFTFQTAQGNDIFQADETAIHRQKAQGKARQGHNALRADSYERKVVEGKF

Parental  PSPPGPQELLDSPPALYAEPLDSLRIAPCPSQDSLYSDPLDSTSAQAGEGVQRKKPLYWDLYEHAQQQLL
          .SPPGPQELL.SPPALYAEPLDSL.IA..PSQ.SLYSD.LD.T.A.AGEGVQ.KKPLYWDLYEH.QQQLL
Retrocopy SSPPGPQELLESPPALYAEPLDSLHIASGPSQGSLYSDLLDGTLAWAGEGVQWKKPLYWDLYEHEQQQLL

Parental  KAKLTDPKEDPIYDEPEGLAPVPPQGLYDLPREPKDAW-WCQARVKEEGYELPYNPATDDYAVPPPRSTK
          KAKLTDPKEDPIYDEPEGLAP..PQGLYDLP.EPKD.W..CQA.VK.EGY.LPYNPATDDYA.PP...TK
Retrocopy KAKLTDPKEDPIYDEPEGLAPALPQGLYDLP*EPKDVW<GCQAQVK*EGYKLPYNPATDDYAMPPTQRTK

Parental  PLLAPKPQGPAFPEPGTATGSGIKSHNSALYSQVQKSGASGSWDCGLSRVGTDKTGVKSEGST
          .L.A.K.QGPAFPEP.TATG...KSHNSALYSQVQKSGASGSWDC.LS.VGTD.TGVKSE.ST
Retrocopy TLPASKSQGPAFPEPSTATGRSSKSHNSALYSQVQKSGASGSWDCVLSTVGTDRTGVKSEVST

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	6.13 RPM
SRP007412_cerebellum	0.14 RPM	10.79 RPM
SRP007412_heart	0.00 RPM	2.16 RPM
SRP007412_kidney	0.00 RPM	5.91 RPM
SRP007412_liver	0.03 RPM	6.87 RPM
SRP007412_testis	0.84 RPM	1.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_615 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_615 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_615 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_891
Macaca mulatta	retro_mmul_1103

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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 ,