RetrogeneDB ID: retro_ptro_2599

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:15447546..15448705(-)
• Located in intron of: ENSPTRG00000018954

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD17
• Ensembl ID: ENSPTRG00000016950
• Aliases: None
• Description: RAD17 homolog (S. pombe) [Source:HGNC Symbol;Acc:9807]

Sequence

>retro_ptro_2599
ATGATGAAATTTCTTAATCGAATAGTGACTATAGAGGCTAACAAGAATGGAGGAAAAATTACTGTCCCTGACAAAACTTC
TCTAGAGGTGCTCTGTCAAGGATGTTCTGGTGATATGAGAAGCGCAATAAACAGCCTCCAGATTTCTTCCTCAAAAGGAG
AAGACAACTTATGGCCAAGGAAAAAAAGAATGTCTTTAAAATCAAATGCTACACTGTCAAAATCGAAACGAAGAAAAAAA
ACTGATAGGGTTTTTGAAAGTCAAGAGGTCCAAGCTACTGGTGGCAAAGACGTTTCTCTGTTTCTCTTCCGAGCTTTGGG
GAAAATTTTATACAGTAAAAGAGCATCTTTAACAGAATCAGACTCAACTCGGTTGCCCTCTCATATATCAGAATATGAAC
AGGATACATACTTGTTGAACCTGAGGAGGTAGTAGAAATGTCACACATGCCAGGAGACTTATTTAATTTATATCTTCACC
AAAACTACATAGATTTCTTCATGGAAACTGATGATATTGTGAGAGCCAGTGAATTTCTAAGTTTTGCAGGTATCCTCAGT
GGTGACTGGAATACACGCTCTTTACTCAGGAAATATAGGACATCTATAGCTACGAGAGGTGTGATACATTCCAACAAAGC
CGGAGGATATGCTCATTGCCAAGGAGAGGATCAAGTTTTTGACCCTTGCACACACCGCAGTGGTTTCTAATACATAAAAA
GTATGGGGAAAATTGCCTGGCAGCAAAAGCACTTTTTCCTGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAGCTAC
TGCCATACCTTGCTCTACTAACTATTCCAATGAGAAATCAAGCTCAGATTTCTCTTATCCAAGATATTGGAAGGCTCCCT
CTGAAGCAACACTCTGGAAGACTGAAAATGGAAGCCCTGACTGACAGGGAACATGGAATGATCGACCCTGACAGTGGAGA
TGAAGCCCAGCTTAACGGAGGACATTCTGCAGACGAATCTCTGGGTGAACCCGCACAGGACACAGAGCTGGAAACCTGGT
CTCTTCCTCTGAGTCAGAATAGTGCCAGTGAACTGCCTGCCAGCCAGCCTCAGCTCTTTTCAGCCCAAGGAGACGTGGAA
GAAAACATAATAATAGAAGACTATGAGAGTGATGGGACA

Alignment

ORF - retro_ptro_2599 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.17 %
• Parental protein coverage: 56.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMKFLNRIVTIEANKNGGKITVPDKTSLELLCQGCSGDIRSAINSLQFSSSKGENNLRPTKKGMSLKSDA
          MMKFLNRIVTIEANKNGGKITVPDKTSLE.LCQGCSGD.RSAINSLQ.SSSKGE.NL.P.KK.MSLKS.A
Retrocopy MMKFLNRIVTIEANKNGGKITVPDKTSLEVLCQGCSGDMRSAINSLQISSSKGEDNLWPRKKRMSLKSNA

Parental  VLSKSKRRKKPDRVFENQEVQAIGGKDVSLFLFRALGKILYCKRASLTELDSPQLPSHLSEYERDT-LLV
          .LSKSKR....DRVFE.QEVQA.GGKDVSLFLFRALGKILY.KRASLTE.DS..LPSH.SEYE.DT..LV
Retrocopy TLSKSKRXXXXDRVFESQEVQATGGKDVSLFLFRALGKILYSKRASLTESDSTRLPSHISEYEQDT<ILV

Parental  EPEEVVEMSHMPGDLFNLYLHQNYIDFFMEIDDIVRASEFLSFADILSGDWNTRSLLREYSTSIATRGVM
          EPEEVVEMSHMPGDLFNLYLHQNYIDFFME.DDIVRASEFLSFA.ILSGDWNTRSLLR.Y.TSIATRGV.
Retrocopy EPEEVVEMSHMPGDLFNLYLHQNYIDFFMETDDIVRASEFLSFAGILSGDWNTRSLLRKYRTSIATRGVI

Parental  HSNKARGYAHCQGG-GSSFRPLHKPQWFLINKKYRENCLAAKALFPDFCLPALCLQTQLLPYLALLTIPM
          HSNKA.GYAHCQG..GSSF.PLH.PQWFLI.KKY.ENCLAAKALFPDFCLPALCLQTQLLPYLALLTIPM
Retrocopy HSNKAGGYAHCQGE<GSSF*PLHTPQWFLIHKKYGENCLAAKALFPDFCLPALCLQTQLLPYLALLTIPM

Parental  RNQAQISFIQDIGRLPLKRHFGRLKMEALTDREHGMIDPGSGDEAQLNGGHSAEESLGEPTQATAPETWS
          RNQAQIS.IQDIGRLPLK.H.GRLKMEALTDREHGMIDP.SGDEAQLNGGHSA.ESLGEP.Q.T..ETWS
Retrocopy RNQAQISLIQDIGRLPLKQHSGRLKMEALTDREHGMIDPDSGDEAQLNGGHSADESLGEPAQDTELETWS

Parental  LPLSQNSASELPASQPQPFSAQGDMEENIIIEDYESDGT
          LPLSQNSASELPASQPQ.FSAQGD.EENIIIEDYESDGT
Retrocopy LPLSQNSASELPASQPQLFSAQGDVEENIIIEDYESDGT

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	7.94 RPM
SRP007412_cerebellum	0.00 RPM	10.15 RPM
SRP007412_heart	0.00 RPM	7.05 RPM
SRP007412_kidney	0.00 RPM	13.81 RPM
SRP007412_liver	0.00 RPM	6.45 RPM
SRP007412_testis	0.00 RPM	91.05 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2599 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2599 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2599 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	ENSG00000152942	1 retrocopy	retro_hsap_3821,
Macaca mulatta	ENSMMUG00000014881	1 retrocopy	retro_mmul_1630,
Nomascus leucogenys	ENSNLEG00000004118	1 retrocopy	retro_nleu_215,
Pan troglodytes	ENSPTRG00000016950	1 retrocopy	retro_ptro_2599 ,