RetrogeneDB - Retrocopy retro_ptro

						
>retro_ptro_2313
TTCGGCAACTCCATGTTTCACAACCGGCACCTCTTTAAAGACAAGGTGGTGCTGGATGTGGGCTCGGATACAAGCATCCT

CTGCATGTTCGCCGCCAAGGCCGGGCCCGCAAGGTCATCGGCATCGAGTGTTCCAGTAGCTCTGATTATGCGGTGAAGAT

TGTCGAAGCCAACAAGTTAGACCACTTGGTGACCATCACCAAGGGGAAGGTGGAGGAGATAGAGCTCCCGGTGGAAAAGG

TGAACATCATCATCAGCAAGTGGATGGGCTAACTGCCTCTTCTACGAGTCCATGCTCAACACTGTGCTCTATGCCCGGAC

AAGTGGCTGGCGCCCAATAGCCTCACCTTCCCAGACCGGGCCACACTGTATGTGACGGCCACCGACGACCGGCAGTACAA

AGACTACAAGATCCACTGGTGGGAGAACGTTTATGGCTTCGATATATCTTGCATCAAAGATGTGGCCGTCAAGGAAACCC

TAGTGGATGTGGTGGACCTCAAACAGCTGGTTACCAACGCCTGCCTCATAAAGGAGGTAGACATCTACACCGTCAAGGTG

GAAGACCTGACCTTCACCTCCCCGTTCTGCCTGCAAGTGAAGCAGAATGACTACGTGCACACCCAGGTGGCCTACTTCAA

CATCGAGTTTATGCACTGCCACAAGAGGACCGGAGGGACCGGCTTCTCCACCATACCCGAGTCCCTGTACACGCACTGGA

AGCAGACGGTGTTCTACATGGAGGACTACCTGACCTTGAAGACAGGCGAGGAGATCTTCGGCACCATCGGCATGCGGCCC

AACGCCAAGAACTGGGACCGGGACTTCACCATCAACCTAGATTTCAGGGGCCATCTGTGCGACCTGTCCTGCTCCACAGA

CTACAGGATG

ORF - retro_ptro_2313 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	71.43 %
Parental protein coverage:	76.62 %
Number of stop codons detected:	0
Number of frameshifts detected	3

Retrocopy - Parental Gene Alignment:

									ParentalYRNSMYHNKHVFKDKVVLDVGSGTGILSMFAAKAG-AKKVFGIECSSISDYSEKIIKANHLDNIITIFKG
		..NSM.HN.H.FKDKVVLDVGS.T.IL.MFAAKAG.A.KV.GIECSS.SDY..KI..AN.LD...TI.KG
RetrocopyFGNSMFHNRHLFKDKVVLDVGSDTSILCMFAAKAG<ARKVIGIECSSSSDYAVKIVEANKLDHLVTITKG
ParentalKVEEVELPVEKVDIIISEWMG-YCLFYESMLNTVIFAR-DKWLKPGGLMFPDRAALYVVAIEDRQYKDFK
		KVEE.ELPVEKV.IIIS.WMG..CLFYESMLNTV..AR.DKWL.P..L.FPDRA.LYV.A..DRQYKD.K
RetrocopyKVEEIELPVEKVNIIISKWMG>NCLFYESMLNTVLYAR<DKWLAPNSLTFPDRATLYVTATDDRQYKDYK
ParentalIHWWENVYGFDMTCIRDVAMKEPLVDIVDPKQVVTNACLIKEVDIYTVKTEELSFTSAFCLQIQRNDYVH
		IHWWENVYGFD..CI.DVA.KE.LVD.VD.KQ.VTNACLIKEVDIYTVK.E.L.FTS.FCLQ...NDYVH
RetrocopyIHWWENVYGFDISCIKDVAVKETLVDVVDLKQLVTNACLIKEVDIYTVKVEDLTFTSPFCLQVKQNDYVH
ParentalALVTYFNIEFTKCHKKMG---FSTAPDAPYTHWKQTVFYLEDYLTVRRGEEIYGTISMKPNAKNVRDLDF
		..V.YFNIEF..CHK..G...FST.P...YTHWKQTVFY.EDYLT...GEEI.GTI.M.PNAKN..D.DF
RetrocopyTQVAYFNIEFMHCHKRTGGTGFSTIPESLYTHWKQTVFYMEDYLTLKTGEEIFGTIGMRPNAKN-WDRDF
ParentalTVDLDFKGQLCETSVSNDYKM
		T..LDF.G.LC..S.S.DY.M
RetrocopyTINLDFRGHLCDLSCSTDYRM

							

							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	13 .41 RPM	39 .70 RPM
SRP007412_cerebellum	15 .41 RPM	25 .24 RPM
SRP007412_heart	28 .65 RPM	0 .03 RPM
SRP007412_kidney	15 .82 RPM	0 .44 RPM
SRP007412_liver	15 .48 RPM	0 .03 RPM
SRP007412_testis	10 .43 RPM	1 .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_2313 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_2313 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_2313 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3406
Gorilla gorilla	retro_ggor_2305
Pongo abelii	retro_pabe_2804
Macaca mulatta	retro_mmul_2121
Callithrix jacchus	retro_cjac_1800

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000004075	1 retrocopy	retro_meug_455,
Nomascus leucogenys	ENSNLEG00000002986	1 retrocopy	retro_nleu_2941,
Pongo abelii	ENSPPYG00000004159	1 retrocopy	retro_pabe_2804,
Pan troglodytes	ENSPTRG00000004543	1 retrocopy	retro_ptro_2313 ,
Tupaia belangeri	ENSTBEG00000000940	1 retrocopy	retro_tbel_750,

	RetrogeneDB ID:	retro_ptro_2313
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	5:178340246..178341136(-)
	Located in intron of:	ENSPTRG00000017575
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	PRMT8
	Ensembl ID:	ENSPTRG00000004543
	Aliases:	None
	Description:	protein arginine methyltransferase 8 [Source:HGNC Symbol;Acc:5188]

Parental	YRNSMYHNKHVFKDKVVLDVGSGTGILSMFAAKAG-AKKVFGIECSSISDYSEKIIKANHLDNIITIFKG
	..NSM.HN.H.FKDKVVLDVGS.T.IL.MFAAKAG.A.KV.GIECSS.SDY..KI..AN.LD...TI.KG
Retrocopy	FGNSMFHNRHLFKDKVVLDVGSDTSILCMFAAKAG<ARKVIGIECSSSSDYAVKIVEANKLDHLVTITKG

Parental	KVEEVELPVEKVDIIISEWMG-YCLFYESMLNTVIFAR-DKWLKPGGLMFPDRAALYVVAIEDRQYKDFK
	KVEE.ELPVEKV.IIIS.WMG..CLFYESMLNTV..AR.DKWL.P..L.FPDRA.LYV.A..DRQYKD.K
Retrocopy	KVEEIELPVEKVNIIISKWMG>NCLFYESMLNTVLYAR<DKWLAPNSLTFPDRATLYVTATDDRQYKDYK

Parental	IHWWENVYGFDMTCIRDVAMKEPLVDIVDPKQVVTNACLIKEVDIYTVKTEELSFTSAFCLQIQRNDYVH
	IHWWENVYGFD..CI.DVA.KE.LVD.VD.KQ.VTNACLIKEVDIYTVK.E.L.FTS.FCLQ...NDYVH
Retrocopy	IHWWENVYGFDISCIKDVAVKETLVDVVDLKQLVTNACLIKEVDIYTVKVEDLTFTSPFCLQVKQNDYVH

Parental	ALVTYFNIEFTKCHKKMG---FSTAPDAPYTHWKQTVFYLEDYLTVRRGEEIYGTISMKPNAKNVRDLDF
	..V.YFNIEF..CHK..G...FST.P...YTHWKQTVFY.EDYLT...GEEI.GTI.M.PNAKN..D.DF
Retrocopy	TQVAYFNIEFMHCHKRTGGTGFSTIPESLYTHWKQTVFYMEDYLTLKTGEEIFGTIGMRPNAKN-WDRDF

Parental	TVDLDFKGQLCETSVSNDYKM
	T..LDF.G.LC..S.S.DY.M
Retrocopy	TINLDFRGHLCDLSCSTDYRM

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

RetrogeneDB ID:

retro_ptro_2313