RetrogeneDB - Retrocopy retro_ptro

						
>retro_ptro_1487
GGTGCTTATTCCCTCTCTATTCGTGATTGGGATGAGGTAAGGGGTGACAATGTGAAACACCACAAAATTAGGAAACTTGA

CAATGGTAGATACTATATCACAACCAGAGAACAATTTGATACTCTGCAGAAATTGGCAAAACACTACACAGAACATGCTG

ATGGTTTATGCCACAAGTTAACAACTGAGTGTCCAACTGTGAAACCTCAGAATCAAGGTCTAGCAAAAGATGCTTGGGAA

ATCCCTTGATAATCTTTGCGACTAGAGGTTAAACTAGGACAAGGATGTTTTGGCATAGTGTGGTTGGGAGTATGGAATGG

AACCACAAAAGTAGCAATCAAAACACTAAAACCAGGTACAATGATGCCAGAAGCTTTTCTTCAAGAAGCTCAGGTAATGA

AAAAAATAAGACATGGTAAACTTGTTCCACTATATGCTGTTGTTTCTGAAGAGCCAATTTACATTGTCACTGAATTGATG

TCAAAAGGAAGCTTACTCAATTTCCTTAAGGAAGGAGATGGAAAGTATTTGAAGCTTCCACAAATGGTTGATATGGCTGC

TCAGACTGCTTATGGTATGGCATATATTGAAAGAATGAATTATATTCACCGAGATCTCTGGGCTGCTAATATTCTTGTAG

GAGAAAATCTTCTGTGCAAAATAGCAGATTTTGGTTTAGCAAGGTTAATTGAAGACAATGAATACACATCAAGACAAGGT

GCAGAATTTCCAATCAAATGGACAGCTCCTGAAGTTGCACTGTATGGTGGGTTTACAATTAAAGTCTGATGTCTGCTCAT

TTGGAATTCTACAGACAGAACTGGTAACAAAGGGCAGAGTGCCATATCCAGGTATGGTGAACCATGAAGTACTGGAACAG

GTGGAGCGAGGATACAGGATGCCTTGCCCTCAGGGCTGTCCAGAATCCCTCCATGAATTGATGAATCTGTGTTGGAAGAA

GGACCCTGATGAAAGACCAACATTTGAATATATTCAGTCCTTCTTGGGAGACTACTTCACTGCTACAGAGCCATAGTACC

AGCCAGGAGAAAAC

ORF - retro_ptro_1487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	91.19 %
Parental protein coverage:	64.64 %
Number of stop codons detected:	3
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalGAYSLSIRDWDEIRGDNVKHYKIRKLDNGGYYITTRAQFDTLQKLVKHYTEHADGLCHKLTTVCPTVKPQ
		GAYSLSIRDWDE.RGDNVKH.KIRKLDNG.YYITTR.QFDTLQKL.KHYTEHADGLCHKLTT.CPTVKPQ
RetrocopyGAYSLSIRDWDEVRGDNVKHHKIRKLDNGRYYITTREQFDTLQKLAKHYTEHADGLCHKLTTECPTVKPQ
ParentalTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTKVAIKTLKPGTMMPEAFLQEAQIMKKLRHDK
		.QGLAKDAWEIP..SLRLEVKLGQGCFG.VW.G.WNGTTKVAIKTLKPGTMMPEAFLQEAQ.MKK.RH.K
RetrocopyNQGLAKDAWEIP**SLRLEVKLGQGCFGIVWLGVWNGTTKVAIKTLKPGTMMPEAFLQEAQVMKKIRHGK
ParentalLVPLYAVVSEEPIYIVTEFMSKGSLLDFLKEGDGKYLKLPQLVDMAAQIADGMAYIERMNYIHRDLRAAN
		LVPLYAVVSEEPIYIVTE.MSKGSLL.FLKEGDGKYLKLPQ.VDMAAQ.A.GMAYIERMNYIHRDL.AAN
RetrocopyLVPLYAVVSEEPIYIVTELMSKGSLLNFLKEGDGKYLKLPQMVDMAAQTAYGMAYIERMNYIHRDLWAAN
ParentalILVGENLVCKIADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTI-KSDVWSFGILQTELVTKGR
		ILVGENL.CKIADFGLARLIEDNEYT.RQGA.FPIKWTAPE.ALYG.FTI.KSDV.SFGILQTELVTKGR
RetrocopyILVGENLLCKIADFGLARLIEDNEYTSRQGAEFPIKWTAPEVALYGGFTI>KSDVCSFGILQTELVTKGR
ParentalVPYPGMVNREVLEQVERGYRMPCPQGCPESLHELMNLCWKKDPDERPTFEYIQSFLEDYFTATEPQYQPG
		VPYPGMVN.EVLEQVERGYRMPCPQGCPESLHELMNLCWKKDPDERPTFEYIQSFL.DYFTATEP.YQPG
RetrocopyVPYPGMVNHEVLEQVERGYRMPCPQGCPESLHELMNLCWKKDPDERPTFEYIQSFLGDYFTATEP*YQPG
ParentalEN
		EN
RetrocopyEN

							

							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 .73 RPM	7 .49 RPM
SRP007412_cerebellum	0 .68 RPM	8 .60 RPM
SRP007412_heart	0 .15 RPM	35 .30 RPM
SRP007412_kidney	0 .16 RPM	78 .43 RPM
SRP007412_liver	0 .03 RPM	46 .12 RPM
SRP007412_testis	0 .21 RPM	40 .89 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_1487 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1487 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_1487 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2551

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000176105	1 retrocopy	retro_hsap_2551,
Monodelphis domestica	ENSMODG00000021477	1 retrocopy	retro_mdom_1121,
Oryctolagus cuniculus	ENSOCUG00000005874	1 retrocopy	retro_ocun_894,
Otolemur garnettii	ENSOGAG00000003375	1 retrocopy	retro_ogar_1684,
Pan troglodytes	ENSPTRG00000009824	1 retrocopy	retro_ptro_1487 ,

	RetrogeneDB ID:	retro_ptro_1487
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	22:24296329..24297383(+)
	Located in intron of:	ENSPTRG00000014187
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	YES1
	Ensembl ID:	ENSPTRG00000009824
	Aliases:	None
	Description:	None

Parental	GAYSLSIRDWDEIRGDNVKHYKIRKLDNGGYYITTRAQFDTLQKLVKHYTEHADGLCHKLTTVCPTVKPQ
	GAYSLSIRDWDE.RGDNVKH.KIRKLDNG.YYITTR.QFDTLQKL.KHYTEHADGLCHKLTT.CPTVKPQ
Retrocopy	GAYSLSIRDWDEVRGDNVKHHKIRKLDNGRYYITTREQFDTLQKLAKHYTEHADGLCHKLTTECPTVKPQ

Parental	TQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTKVAIKTLKPGTMMPEAFLQEAQIMKKLRHDK
	.QGLAKDAWEIP..SLRLEVKLGQGCFG.VW.G.WNGTTKVAIKTLKPGTMMPEAFLQEAQ.MKK.RH.K
Retrocopy	NQGLAKDAWEIP**SLRLEVKLGQGCFGIVWLGVWNGTTKVAIKTLKPGTMMPEAFLQEAQVMKKIRHGK

Parental	LVPLYAVVSEEPIYIVTEFMSKGSLLDFLKEGDGKYLKLPQLVDMAAQIADGMAYIERMNYIHRDLRAAN
	LVPLYAVVSEEPIYIVTE.MSKGSLL.FLKEGDGKYLKLPQ.VDMAAQ.A.GMAYIERMNYIHRDL.AAN
Retrocopy	LVPLYAVVSEEPIYIVTELMSKGSLLNFLKEGDGKYLKLPQMVDMAAQTAYGMAYIERMNYIHRDLWAAN

Parental	ILVGENLVCKIADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTI-KSDVWSFGILQTELVTKGR
	ILVGENL.CKIADFGLARLIEDNEYT.RQGA.FPIKWTAPE.ALYG.FTI.KSDV.SFGILQTELVTKGR
Retrocopy	ILVGENLLCKIADFGLARLIEDNEYTSRQGAEFPIKWTAPEVALYGGFTI>KSDVCSFGILQTELVTKGR

Parental	VPYPGMVNREVLEQVERGYRMPCPQGCPESLHELMNLCWKKDPDERPTFEYIQSFLEDYFTATEPQYQPG
	VPYPGMVN.EVLEQVERGYRMPCPQGCPESLHELMNLCWKKDPDERPTFEYIQSFL.DYFTATEP.YQPG
Retrocopy	VPYPGMVNHEVLEQVERGYRMPCPQGCPESLHELMNLCWKKDPDERPTFEYIQSFLGDYFTATEP*YQPG

Parental	EN
	EN
Retrocopy	EN

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

RetrogeneDB ID:

retro_ptro_1487