RetrogeneDB - Retrocopy retro_ptro

						
>retro_ptro_1776
TCAGGTGTCACAGAAACAGCCCAGTGTGGCCAGGGTGCAAAACCTCAAGTTCAAGTGAAGAGGAAGCTGAAAACTGGAAT

ATTAATGCTAAACATGGGAGGACCTGAAACCCTCTGACAGGTTCATGACTTCCTTCTGAGGCTCTTTTTGGACCAAGACC

TCATGACACTTACTGTTCAAAATAAGTTTACACCATTCTTTGCCAAATGCAGAACCTCCAAGATTCAAGGGCAGTACCAC

AGAACTGGAGGTGGGTCCTCCATCAAGACGTGGATTTCCAAGCAGGGAGAAGGCATGGTGAAGCTGCTGGATGACTTGTC

CCCCTACACAGCCCCTCACAAATAATACTTCATTGGATTTTGGCATGTCCATTCTTTACTAAAAGAAGCAAATGAAGAGA

TGGAGAGAGATGGCCTGGAAAGGGATATTGCTTTCATGCAGGATCCACAGTACGCTTGCTGTACCACAGGCGGCAGCTTA

AATGCCATTTAAAGATCCTATAATAGAGTGGGACGGAAGTTTACAATGATGTGCAGCACTATCAGTAGGTGGCCCACCCA

TTGCCTCCTCACCCACTGCTTTGTTGACTACATTCTGAAAGAGCTGGACCATTTTCCACTGGAGAAGAGAAGCGAGTCGG

CCATTCTCTTTTCTGCTCACTCACTGCCAATATCCATGATCAACAGAGGAGACCCCTGTTCTCAGGAGTTAAGTGCCACT

ATCCAAAGAGTCATAGAAAGGCTGGGTTACTGCAACCCTTACCAGCTGGTGTGAGGATCCAAGGTTGGTTCAGTGCCCTG

GATGGGTCTTCAAACAGATGAAATCTATCAGAGGGCTTTCTGAGAGGGGGAAGAATATCCTCTCACTTTTGATAGCATTT

ACCAACGATAACACCAAAATGCTGTAGAAACTGGATATCGAGTACGCTCAAGTTTTAGACAATGAGTGTGGAGTTGAAAA

CATCAGAAGAGCAGCCTCT

ORF - retro_ptro_1776 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	72.64 %
Parental protein coverage:	86.28 %
Number of stop codons detected:	5
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalAATTETAQHAQGAKPQVQPQKRKPKTGILMLNMGGPETLGDVHDFLLRLFLDRDLMTLPIQNKLAPFIAK
		...TETAQ..QGAKPQVQ..KRK.KTGILMLNMGGPETL..VHDFLLRLFLD.DLMTL..QNK..PF.AK
RetrocopySGVTETAQCGQGAKPQVQV-KRKLKTGILMLNMGGPETL*QVHDFLLRLFLDQDLMTLTVQNKFTPFFAK
ParentalRRTPKIQEQYRRIGGGSPIKIWTSKQGEGMVKLLDELSPNTAPHK-YYIGFRYVHPLTEEAIEEMERDGL
		.RT.KIQ.QY.R.GGGS.IK.W.SKQGEGMVKLLD.LSP.TAPHK.Y.IGF..VH.L..EA.EEMERDGL
RetrocopyCRTSKIQGQYHRTGGGSSIKTWISKQGEGMVKLLDDLSPYTAPHK*YFIGFWHVHSLLKEANEEMERDGL
ParentalERAIAFTQYPQYSCSTTGSSLNAIYRYYNQVGQKPTMKWSTIDRWPTHHLLIQCFADHILKELDHFPLEK
		ER.IAF.Q.PQY.C.TTG.SLNAI.R.YN.VG.K.TM..STI.RWPTH.LL..CF.D.ILKELDHFPLEK
RetrocopyERDIAFMQDPQYACCTTGGSLNAI*RSYNRVGRKFTMMCSTISRWPTHCLLTHCFVDYILKELDHFPLEK
ParentalRSEVVILFSAHSLPMSVVNRGDPYPQEVSATVQKVMERLEYCNPYRLVWQSKVGPMPWLGPQTDE-SIKG
		RSE..ILFSAHSLP.S..NRGDP..QE.SAT.Q.V.ERL.YCNPY.LV..SKVG..PW.G.QTDE.SI.G
RetrocopyRSESAILFSAHSLPISMINRGDPCSQELSATIQRVIERLGYCNPYQLV*GSKVGSVPWMGLQTDE>SIRG
ParentalLCERGRKNILLVPIAFTSDHIETLYELDIEYSQVLAKECGVENIRRAES
		L.ERG.KNIL...IAFT.D....L..LDIEY.QVL..ECGVENIRRA.S
RetrocopyLSERG-KNILSLLIAFTNDNTKML*KLDIEYAQVLDNECGVENIRRAAS

							

							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	6 .54 RPM
SRP007412_cerebellum	0 .00 RPM	4 .52 RPM
SRP007412_heart	0 .00 RPM	8 .92 RPM
SRP007412_kidney	0 .00 RPM	18 .88 RPM
SRP007412_liver	0 .00 RPM	7 .69 RPM
SRP007412_testis	0 .00 RPM	5 .37 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_1776 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1776 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_1776 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2631
Gorilla gorilla	retro_ggor_1841
Pongo abelii	retro_pabe_2332
Macaca mulatta	retro_mmul_1485

Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003873	1 retrocopy	retro_cjac_4008,
Homo sapiens	ENSG00000066926	1 retrocopy	retro_hsap_2631,
Gorilla gorilla	ENSGGOG00000005554	1 retrocopy	retro_ggor_1841,
Macaca mulatta	ENSMMUG00000022568	1 retrocopy	retro_mmul_1485,
Nomascus leucogenys	ENSNLEG00000008062	1 retrocopy	retro_nleu_643,
Oryctolagus cuniculus	ENSOCUG00000003020	1 retrocopy	retro_ocun_497,
Pongo abelii	ENSPPYG00000009182	1 retrocopy	retro_pabe_2332,
Pan troglodytes	ENSPTRG00000010045	1 retrocopy	retro_ptro_1776 ,

	RetrogeneDB ID:	retro_ptro_1776
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	3:35438428..35439407(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	FECH
	Ensembl ID:	ENSPTRG00000010045
	Aliases:	None
	Description:	Pan troglodytes ferrochelatase (FECH), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001038012]

Parental	AATTETAQHAQGAKPQVQPQKRKPKTGILMLNMGGPETLGDVHDFLLRLFLDRDLMTLPIQNKLAPFIAK
	...TETAQ..QGAKPQVQ..KRK.KTGILMLNMGGPETL..VHDFLLRLFLD.DLMTL..QNK..PF.AK
Retrocopy	SGVTETAQCGQGAKPQVQV-KRKLKTGILMLNMGGPETL*QVHDFLLRLFLDQDLMTLTVQNKFTPFFAK

Parental	RRTPKIQEQYRRIGGGSPIKIWTSKQGEGMVKLLDELSPNTAPHK-YYIGFRYVHPLTEEAIEEMERDGL
	.RT.KIQ.QY.R.GGGS.IK.W.SKQGEGMVKLLD.LSP.TAPHK.Y.IGF..VH.L..EA.EEMERDGL
Retrocopy	CRTSKIQGQYHRTGGGSSIKTWISKQGEGMVKLLDDLSPYTAPHK*YFIGFWHVHSLLKEANEEMERDGL

Parental	ERAIAFTQYPQYSCSTTGSSLNAIYRYYNQVGQKPTMKWSTIDRWPTHHLLIQCFADHILKELDHFPLEK
	ER.IAF.Q.PQY.C.TTG.SLNAI.R.YN.VG.K.TM..STI.RWPTH.LL..CF.D.ILKELDHFPLEK
Retrocopy	ERDIAFMQDPQYACCTTGGSLNAI*RSYNRVGRKFTMMCSTISRWPTHCLLTHCFVDYILKELDHFPLEK

Parental	RSEVVILFSAHSLPMSVVNRGDPYPQEVSATVQKVMERLEYCNPYRLVWQSKVGPMPWLGPQTDE-SIKG
	RSE..ILFSAHSLP.S..NRGDP..QE.SAT.Q.V.ERL.YCNPY.LV..SKVG..PW.G.QTDE.SI.G
Retrocopy	RSESAILFSAHSLPISMINRGDPCSQELSATIQRVIERLGYCNPYQLV*GSKVGSVPWMGLQTDE>SIRG

Parental	LCERGRKNILLVPIAFTSDHIETLYELDIEYSQVLAKECGVENIRRAES
	L.ERG.KNIL...IAFT.D....L..LDIEY.QVL..ECGVENIRRA.S
Retrocopy	LSERG-KNILSLLIAFTNDNTKML*KLDIEYAQVLDNECGVENIRRAAS

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

RetrogeneDB ID:

retro_ptro_1776