RetrogeneDB - Retrocopy retro_ptro

                        
>retro_ptro_2599
ATGATGAAATTTCTTAATCGAATAGTGACTATAGAGGCTAACAAGAATGGAGGAAAAATTACTGTCCCTGACAAAACTTC

TCTAGAGGTGCTCTGTCAAGGATGTTCTGGTGATATGAGAAGCGCAATAAACAGCCTCCAGATTTCTTCCTCAAAAGGAG

AAGACAACTTATGGCCAAGGAAAAAAAGAATGTCTTTAAAATCAAATGCTACACTGTCAAAATCGAAACGAAGAAAAAAA

ACTGATAGGGTTTTTGAAAGTCAAGAGGTCCAAGCTACTGGTGGCAAAGACGTTTCTCTGTTTCTCTTCCGAGCTTTGGG

GAAAATTTTATACAGTAAAAGAGCATCTTTAACAGAATCAGACTCAACTCGGTTGCCCTCTCATATATCAGAATATGAAC

AGGATACATACTTGTTGAACCTGAGGAGGTAGTAGAAATGTCACACATGCCAGGAGACTTATTTAATTTATATCTTCACC

AAAACTACATAGATTTCTTCATGGAAACTGATGATATTGTGAGAGCCAGTGAATTTCTAAGTTTTGCAGGTATCCTCAGT

GGTGACTGGAATACACGCTCTTTACTCAGGAAATATAGGACATCTATAGCTACGAGAGGTGTGATACATTCCAACAAAGC

CGGAGGATATGCTCATTGCCAAGGAGAGGATCAAGTTTTTGACCCTTGCACACACCGCAGTGGTTTCTAATACATAAAAA

GTATGGGGAAAATTGCCTGGCAGCAAAAGCACTTTTTCCTGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAGCTAC

TGCCATACCTTGCTCTACTAACTATTCCAATGAGAAATCAAGCTCAGATTTCTCTTATCCAAGATATTGGAAGGCTCCCT

CTGAAGCAACACTCTGGAAGACTGAAAATGGAAGCCCTGACTGACAGGGAACATGGAATGATCGACCCTGACAGTGGAGA

TGAAGCCCAGCTTAACGGAGGACATTCTGCAGACGAATCTCTGGGTGAACCCGCACAGGACACAGAGCTGGAAACCTGGT

CTCTTCCTCTGAGTCAGAATAGTGCCAGTGAACTGCCTGCCAGCCAGCCTCAGCTCTTTTCAGCCCAAGGAGACGTGGAA

GAAAACATAATAATAGAAGACTATGAGAGTGATGGGACA

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:

                                ParentalMMKFLNRIVTIEANKNGGKITVPDKTSLELLCQGCSGDIRSAINSLQFSSSKGENNLRPTKKGMSLKSDA
MMKFLNRIVTIEANKNGGKITVPDKTSLE.LCQGCSGD.RSAINSLQ.SSSKGE.NL.P.KK.MSLKS.A
RetrocopyMMKFLNRIVTIEANKNGGKITVPDKTSLEVLCQGCSGDMRSAINSLQISSSKGEDNLWPRKKRMSLKSNA
ParentalVLSKSKRRKKPDRVFENQEVQAIGGKDVSLFLFRALGKILYCKRASLTELDSPQLPSHLSEYERDT-LLV
.LSKSKR....DRVFE.QEVQA.GGKDVSLFLFRALGKILY.KRASLTE.DS..LPSH.SEYE.DT..LV
RetrocopyTLSKSKRXXXXDRVFESQEVQATGGKDVSLFLFRALGKILYSKRASLTESDSTRLPSHISEYEQDT<ILV
ParentalEPEEVVEMSHMPGDLFNLYLHQNYIDFFMEIDDIVRASEFLSFADILSGDWNTRSLLREYSTSIATRGVM
EPEEVVEMSHMPGDLFNLYLHQNYIDFFME.DDIVRASEFLSFA.ILSGDWNTRSLLR.Y.TSIATRGV.
RetrocopyEPEEVVEMSHMPGDLFNLYLHQNYIDFFMETDDIVRASEFLSFAGILSGDWNTRSLLRKYRTSIATRGVI
ParentalHSNKARGYAHCQGG-GSSFRPLHKPQWFLINKKYRENCLAAKALFPDFCLPALCLQTQLLPYLALLTIPM
HSNKA.GYAHCQG..GSSF.PLH.PQWFLI.KKY.ENCLAAKALFPDFCLPALCLQTQLLPYLALLTIPM
RetrocopyHSNKAGGYAHCQGE<GSSF*PLHTPQWFLIHKKYGENCLAAKALFPDFCLPALCLQTQLLPYLALLTIPM
ParentalRNQAQISFIQDIGRLPLKRHFGRLKMEALTDREHGMIDPGSGDEAQLNGGHSAEESLGEPTQATAPETWS
RNQAQIS.IQDIGRLPLK.H.GRLKMEALTDREHGMIDP.SGDEAQLNGGHSA.ESLGEP.Q.T..ETWS
RetrocopyRNQAQISLIQDIGRLPLKQHSGRLKMEALTDREHGMIDPDSGDEAQLNGGHSADESLGEPAQDTELETWS
ParentalLPLSQNSASELPASQPQPFSAQGDMEENIIIEDYESDGT
LPLSQNSASELPASQPQ.FSAQGD.EENIIIEDYESDGT
RetrocopyLPLSQNSASELPASQPQLFSAQGDVEENIIIEDYESDGT

                            

                            Legend:
                            
                                *Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide

                        

RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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 - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_2599 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_2599 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_2599 has 0 orthologous retrocopies within eutheria group .

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 ,

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

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

*	Stop codon
>	Forward frameshift by one nucleotide
<	Reverse frameshift by one nucleotide

RetrogeneDB ID:

retro_ptro_2599