RetrogeneDB - Retrocopy retro_mmul

						
>retro_mmul_2050
ACTGGAGTTATAAACTGCATCTGCTAGAAAATACTGAGCAATGTCAAGTTTTTATCCATTGCTCCAAATGCAGCAAGAGA

ACTGAGCTTTACCTCAATACTCAAGAAGCTGCAAGATACCATTGAGCAGAGAATAAAAATTGAAATTGGGGACATGTTCT

GAATCAGAGGCTATGTCCGCACATGCAGAGAAGAGTGAGAAATTTATGCCACTGCTTATTATAAAGTGGACGATCCAGTG

TGGAACATTCAAATTGCAAGGGCATTTGAGCTGCCCGTTAATCTACAGGAAAGTTTAGACCAAGTCTTTCCATAGCCCAG

ACTTAGAGAAAGAAGCACTAAGCAAACCAGGTGCCCTGGCCCTCACTAGTCTCATGCATTTGCTGAGCGAAAAAGCCAAA

GAATTCCCCATGGAGAACAGAGTGCAGACCTTTGACCAACAGGAGTTGGAAATGGTGGAGGCTTTGCTGTCCCTTGCTAA

CCAGCCTCTTACTGACAGCACCTGCTCTGACCTAGGGAATTTTAAGAAGGATATCACTTTCAAGGCAATTTATAGCATAT

TTTAAAATGTTATGCAACAGCTGCAGGAAAAAGGACTTGTTTTCCAGAAAGATGGTGGTTTTCATAACCTATGCTGTGTA

ACCAGAACAGACAAAGACCTGCATAGGAAAATCCACTGGATAATTCAGGAAGACTGCCAGAAACCAAATCACCCGAAGAA

GGGCTGCCACTTCCTGCACATCTTGGCCTGCACTCACCCTGATCATCTGCCCAGTCCTAGGTAGGGCTATGCTGCAGCAA

GTTCTGGAGCTCCTGGAGGACCAGAGTGACCTCATCAACACAATGGAGCACCACTATTCC

ORF - retro_mmul_2050 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	71.28 %
Parental protein coverage:	77.72 %
Number of stop codons detected:	5
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalTGVINCICWKKL-NTESVSAAPSAARELSLTSQLKKLQETIERRTKIEIGDTIRVRGSIRTYREEREIHA
		TGVINCIC.K.L.N....S.AP.AARELS.TS.LKKLQ.TIE.R.KIEIGD....RG..RT.REE.EI.A
RetrocopyTGVINCIC*KILSNVKFLSIAPNAARELSFTSILKKLQDTIEQRIKIEIGDMF*IRGYVRTCREE*EIYA
ParentalTAYYKVDDPVWNIQIARMLELPT-IYRKIYDQPFRSSALEKEEALSNPGALDLPSLTSLLSEKAKEFLME
		TAYYKVDDPVWNIQIAR..ELP..IYRK.....F.S..LEKE.ALS.PGAL.L.SL..LLSEKAKEF.ME
RetrocopyTAYYKVDDPVWNIQIARAFELPV>IYRKV*TKSFHSPDLEKE-ALSKPGALALTSLMHLLSEKAKEFPME
ParentalNRVQSFYQQELEMVESLLCLANQPVIHSACSDQVNFKKDTTSKAIHSIFKNAIQLLREKGLVFQKDDGFD
		NRVQ.F.QQELEMVE.LL.LANQP...S.CSD..NFKKD.T.KAI.SIF.N..Q.L.EKGLVFQKD.GF.
RetrocopyNRVQTFDQQELEMVEALLSLANQPLTDSTCSDLGNFKKDITFKAIYSIF*NVMQQLQEKGLVFQKDGGFH
ParentalNLYYVTREDKDLHRKIHQIIQQDCQKPNHMEKGCHFLHILACAR-LSIRPGLSEAVLQQVLELLEDQSDI
		NL..VTR.DKDLHRKIH.IIQ.DCQKPNH..KGCHFLHILAC...L.I.P.L..A.LQQVLELLEDQSD.
RetrocopyNLCCVTRTDKDLHRKIHWIIQEDCQKPNHPKKGCHFLHILACTH>LIICPVLGRAMLQQVLELLEDQSDL
ParentalVSTMEHYYT
		..TMEH.Y.
RetrocopyINTMEHHYS

							

							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	0 .11 RPM	6 .84 RPM
SRP007412_brain_prefrontal_cortex	0 .08 RPM	4 .68 RPM
SRP007412_cerebellum	0 .00 RPM	4 .46 RPM
SRP007412_heart	0 .06 RPM	19 .73 RPM
SRP007412_kidney	0 .00 RPM	14 .55 RPM
SRP007412_liver	0 .04 RPM	9 .26 RPM
SRP007412_testis	0 .04 RPM	29 .93 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_2050 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_2050 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_mmul_2050 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3257
Pan troglodytes	retro_ptro_2203
Gorilla gorilla	retro_ggor_2219
Pongo abelii	retro_pabe_2701
Callithrix jacchus	retro_cjac_1791

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018342	1 retrocopy	retro_cjac_1791,
Homo sapiens	ENSG00000107960	1 retrocopy	retro_hsap_3257,
Gorilla gorilla	ENSGGOG00000008979	1 retrocopy	retro_ggor_2219,
Macaca mulatta	ENSMMUG00000015323	1 retrocopy	retro_mmul_2050 ,
Nomascus leucogenys	ENSNLEG00000015282	1 retrocopy	retro_nleu_2689,
Pongo abelii	ENSPPYG00000002628	1 retrocopy	retro_pabe_2701,
Pan troglodytes	ENSPTRG00000002919	1 retrocopy	retro_ptro_2203,

	RetrogeneDB ID:	retro_mmul_2050
Retrocopy location	Organism:	*Rhesus macaque (Macaca mulatta)*
	Coordinates:	6:151755681..151756541(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	OBFC1
	Ensembl ID:	ENSMMUG00000015323
	Aliases:	None
	Description:	CST complex subunit STN1 [Source:RefSeq peptide;Acc:NP_001253519]

Parental	TGVINCICWKKL-NTESVSAAPSAARELSLTSQLKKLQETIERRTKIEIGDTIRVRGSIRTYREEREIHA
	TGVINCIC.K.L.N....S.AP.AARELS.TS.LKKLQ.TIE.R.KIEIGD....RG..RT.REE.EI.A
Retrocopy	TGVINCICKILSNVKFLSIAPNAARELSFTSILKKLQDTIEQRIKIEIGDMFIRGYVRTCREE*EIYA

Parental	TAYYKVDDPVWNIQIARMLELPT-IYRKIYDQPFRSSALEKEEALSNPGALDLPSLTSLLSEKAKEFLME
	TAYYKVDDPVWNIQIAR..ELP..IYRK.....F.S..LEKE.ALS.PGAL.L.SL..LLSEKAKEF.ME
Retrocopy	TAYYKVDDPVWNIQIARAFELPV>IYRKV*TKSFHSPDLEKE-ALSKPGALALTSLMHLLSEKAKEFPME

Parental	NRVQSFYQQELEMVESLLCLANQPVIHSACSDQVNFKKDTTSKAIHSIFKNAIQLLREKGLVFQKDDGFD
	NRVQ.F.QQELEMVE.LL.LANQP...S.CSD..NFKKD.T.KAI.SIF.N..Q.L.EKGLVFQKD.GF.
Retrocopy	NRVQTFDQQELEMVEALLSLANQPLTDSTCSDLGNFKKDITFKAIYSIF*NVMQQLQEKGLVFQKDGGFH

Parental	NLYYVTREDKDLHRKIHQIIQQDCQKPNHMEKGCHFLHILACAR-LSIRPGLSEAVLQQVLELLEDQSDI
	NL..VTR.DKDLHRKIH.IIQ.DCQKPNH..KGCHFLHILAC...L.I.P.L..A.LQQVLELLEDQSD.
Retrocopy	NLCCVTRTDKDLHRKIHWIIQEDCQKPNHPKKGCHFLHILACTH>LIICPVLGRAMLQQVLELLEDQSDL

Parental	VSTMEHYYT
	..TMEH.Y.
Retrocopy	INTMEHHYS

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

RetrogeneDB ID:

retro_mmul_2050