RetrogeneDB - Retrocopy retro_pabe

						
>retro_pabe_752
ATTCACCCTGAAAATGAAGATTGGACCTGTTTTGAACAGTCTGCAAGTTTAGATATTAAATCTTTCTTTGGTTTTGAAAG

TACCATGGAAAAAACTGCAGTGAAACAATATATCAGCAATATTAAAAAAAGGAAAGAAAATCATTGAATACTACCTTCGC

CATTTAGAAGAAGGCATAACCTTTGTGCCCCGTTGGACTCCGCCTTCCATCACACCCTCTTCAGAGACATCTTCGTCATC

CTGCAAGAAACAAGCAGTGTCCATGGCCGTTGTCATCCCAGATGCTGTTCTCAAGGAGGGGCTGAGTGGTGATGCCCTCA

GCAGTCCCAGCGCACCTGAGCCCATGGGCACCCCGATAACAAACTAGATGCCGACTACATCAAGAGATACCTGGGCGATC

TGACTCCGCTGCAGGAGAGCTGTCTCATTAGACTTCACCGGTGGCTCCAGGAGACCCACAAGGGCGAAATTCCAAAAGAT

GAGCATATTCTTCAGTTCCTACGTGCGTGGGATTTTAATATTGACAAAGCCAGAGAGATCATTTGTCAATCTTTGGCGTG

GAGGAAGCAGCACCAGGTAGACTACATTCTTGCTACTGGACCGCTCCACAGGTCCTTCAGGATTACTACACGGGAAGCTG

GCATCATCACGACAAAGATGGGCGGCCCCTCTGTGTGCTCAGGCTGGGGCAGATGGACACCAATGGCTTGGTGAGAGCGC

TCGGGGAGGAAGCCCTGCTGAGATATGTTCTCTCCATAAATGAAGAAGAGCTAAGGCGATGTGAAGAGAATACAAAAGTC

TTTGTTTGGCCTATCAGCTCATGGACCTGCCTGGTGGACTTGGAAGGGGTGAACATGCGCCACTTGTGGAGACCTGATGT

CAAAGTGCTGTGGTGGATCATCGAGGTGGTGAAGGCCAATTACCCTAAGAGACTGGGCCGACTTCTCATCCTGCGGGCAC

CCAGGGTATTTCCTGTGCTCTGGACGCTGGTTAGTCCATTTATTGATGACAACACCAGAAGGAAACTCCTCATTTATGCA

GGAAATGACTACCAGGGTCCTGGAGGCCTGCTGGATTACATTGACAGA

ORF - retro_pabe_752 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	88.32 %
Parental protein coverage:	54.07 %
Number of stop codons detected:	0
Number of frameshifts detected	3

Retrocopy - Parental Gene Alignment:

									ParentalVHPENEDWTCFEQSASLDIKSFFGFESTVEKIAMKQYTSNIKK-GKEIIEYYLRQLEEEGITFVPRWTPP
		.HPENEDWTCFEQSASLDIKSFFGFEST.EK.A.KQY.SNIKK.GK.IIEYYLR.LEE.GITFVPRWTPP
RetrocopyIHPENEDWTCFEQSASLDIKSFFGFESTMEKTAVKQYISNIKK>GKKIIEYYLRHLEE-GITFVPRWTPP
ParentalSITPSSETSSSSCKKQAASMAVVIPEAALKEGLSGDALSSPSAPEPVVGTP-DDKLDADYIKRYLGDLTP
		SITPSSETSSSSCKKQA.SMAVVIP.A.LKEGLSGDALSSPSAPEP..GTP.D.KLDADYIKRYLGDLTP
RetrocopySITPSSETSSSSCKKQAVSMAVVIPDAVLKEGLSGDALSSPSAPEP-MGTP<DNKLDADYIKRYLGDLTP
ParentalLQESCLIRLRQWLQETHKGKIPKDEHILRFLRARDFNIDKAREIMCQSLTWRKQHQVDYILET-WTPPQV
		LQESCLIRL..WLQETHKG.IPKDEHIL.FLRA.DFNIDKAREI.CQSL.WRKQHQVDYIL.T.WT.PQV
RetrocopyLQESCLIRLHRWLQETHKGEIPKDEHILQFLRAWDFNIDKAREIICQSLAWRKQHQVDYILAT<WTAPQV
ParentalLQDYYAGGWHHHDKDGRPLYVLRLGQMDTKGLVRALGEEALLRYVLSINEEGLRRCEENTKVFGRPISSW
		LQDYY.G.WHHHDKDGRPL.VLRLGQMDT.GLVRALGEEALLRYVLSINEE.LRRCEENTKVF..PISSW
RetrocopyLQDYYTGSWHHHDKDGRPLCVLRLGQMDTNGLVRALGEEALLRYVLSINEEELRRCEENTKVFVWPISSW
ParentalTCLVDLEGLNMRHLWRPGVKALLRIIEVVEANYPETLGRLLILRAPRVFPVLWTLVSPFIDDNTRRKFLI
		TCLVDLEG.NMRHLWRP.VK.L..IIEVV.ANYP..LGRLLILRAPRVFPVLWTLVSPFIDDNTRRK.LI
RetrocopyTCLVDLEGVNMRHLWRPDVKVLWWIIEVVKANYPKRLGRLLILRAPRVFPVLWTLVSPFIDDNTRRKLLI
ParentalYAGNDYQGPGGLLDYIDK
		YAGNDYQGPGGLLDYID.
RetrocopyYAGNDYQGPGGLLDYIDR

							

							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	2 .93 RPM	118 .32 RPM
SRP007412_cerebellum	5 .72 RPM	50 .46 RPM
SRP007412_heart	1 .20 RPM	25 .62 RPM
SRP007412_kidney	2 .72 RPM	66 .49 RPM
SRP007412_liver	2 .36 RPM	24 .54 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_752 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_752 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_pabe_752 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000129657	1 retrocopy	retro_hsap_777,
Nomascus leucogenys	ENSNLEG00000007634	1 retrocopy	retro_nleu_403,
Pongo abelii	ENSPPYG00000008673	1 retrocopy	retro_pabe_752 ,

	RetrogeneDB ID:	retro_pabe_752
Retrocopy location	Organism:	*Orangutan (Pongo abelii)*
	Coordinates:	11:24854157..24855245(-)
	Located in intron of:	ENSPPYG00000003342
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	SEC14L1
	Ensembl ID:	ENSPPYG00000008673
	Aliases:	None
	Description:	SEC14-like 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:10698]

Parental	VHPENEDWTCFEQSASLDIKSFFGFESTVEKIAMKQYTSNIKK-GKEIIEYYLRQLEEEGITFVPRWTPP
	.HPENEDWTCFEQSASLDIKSFFGFEST.EK.A.KQY.SNIKK.GK.IIEYYLR.LEE.GITFVPRWTPP
Retrocopy	IHPENEDWTCFEQSASLDIKSFFGFESTMEKTAVKQYISNIKK>GKKIIEYYLRHLEE-GITFVPRWTPP

Parental	SITPSSETSSSSCKKQAASMAVVIPEAALKEGLSGDALSSPSAPEPVVGTP-DDKLDADYIKRYLGDLTP
	SITPSSETSSSSCKKQA.SMAVVIP.A.LKEGLSGDALSSPSAPEP..GTP.D.KLDADYIKRYLGDLTP
Retrocopy	SITPSSETSSSSCKKQAVSMAVVIPDAVLKEGLSGDALSSPSAPEP-MGTP<DNKLDADYIKRYLGDLTP

Parental	LQESCLIRLRQWLQETHKGKIPKDEHILRFLRARDFNIDKAREIMCQSLTWRKQHQVDYILET-WTPPQV
	LQESCLIRL..WLQETHKG.IPKDEHIL.FLRA.DFNIDKAREI.CQSL.WRKQHQVDYIL.T.WT.PQV
Retrocopy	LQESCLIRLHRWLQETHKGEIPKDEHILQFLRAWDFNIDKAREIICQSLAWRKQHQVDYILAT<WTAPQV

Parental	LQDYYAGGWHHHDKDGRPLYVLRLGQMDTKGLVRALGEEALLRYVLSINEEGLRRCEENTKVFGRPISSW
	LQDYY.G.WHHHDKDGRPL.VLRLGQMDT.GLVRALGEEALLRYVLSINEE.LRRCEENTKVF..PISSW
Retrocopy	LQDYYTGSWHHHDKDGRPLCVLRLGQMDTNGLVRALGEEALLRYVLSINEEELRRCEENTKVFVWPISSW

Parental	TCLVDLEGLNMRHLWRPGVKALLRIIEVVEANYPETLGRLLILRAPRVFPVLWTLVSPFIDDNTRRKFLI
	TCLVDLEG.NMRHLWRP.VK.L..IIEVV.ANYP..LGRLLILRAPRVFPVLWTLVSPFIDDNTRRK.LI
Retrocopy	TCLVDLEGVNMRHLWRPDVKVLWWIIEVVKANYPKRLGRLLILRAPRVFPVLWTLVSPFIDDNTRRKLLI

Parental	YAGNDYQGPGGLLDYIDK
	YAGNDYQGPGGLLDYID.
Retrocopy	YAGNDYQGPGGLLDYIDR

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

RetrogeneDB ID:

retro_pabe_752