RetrogeneDB - Retrocopy retro_mmul

						
>retro_mmul_1511
ATGGCGCAAGCTGGAGGTGGAGCAGCGGTGCCCAGGATGCCAGTGGGTCCTGGGAGTCCCCGGCGGGTGCAGCGGCGGCA

CCAAGGGCAGCCGCTGGGAAAGCAGCGCCCAGTCCCGTGGTCCGGGCTTCGCAGCAAAGAGAAGAAAGTGAATTGCACGC

CCAAGAACCAGGACGAAGAGGAGATCCCTTTCTGGCTCCGGGAGATTATGGGGAGCTGCCAGAAGATGAAAAACCCGATC

GGTAACAAGAAGAGGAAGAAAGCAGCCCAGGTGGCCTTCAGAAAGACATTGGAGAAGGAAGCAAAGGGAGTGGAGCCCGA

CATCGCCATCCCCAAGTTCAAGCAGAGGAAAGGGGAGTCTGACTAGGCCTATATCCAGCGCATGCAGCAAGAGGTCCAGC

ACATGCTATTCCTCAGCAAGAACCAGGCCACCCGGCAGCCAGACGTCCAGGCAGCTCCCAAGGAGAAGTCTGAGAAAAGT

CTGAGAAAAAAGCAAAAAAAGCATTCCAGAAGCGACGACTAGATAAAGTCCAGCAGAAAAAGGAGGAAAAGATGGCAGAC

AGGCTGGAGCAGGAGTTGCTCAGAGACACGATGAAGTTTGGTGAGGTTGTCCTGCAGCCTCCAGAGCTGACCACCAGGCC

TGGGAGGAGCATAAGCAAGGACCAGCCTGGCAGGAGATCGCAGATGCTGAGGATGCTTCTGAGCTTTGGCAGTGTGTCTC

AGCCTCTGACTGCCTCCCTGGCCTACCAGCGGATTGTGGGGAGGAGAGATAGGAGGCCGTGCAGGCCTACAGAGCATTGA

AGCAGCGACTGCTGCAAGAGGAGCGACCCCACCTCACTTCCCGGAAGAAGCGAGAGCCACAG

ORF - retro_mmul_1511 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	72.01 %
Parental protein coverage:	99.65 %
Number of stop codons detected:	3
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalMARAGRGAAVPRAQAGPGSPRRARRRQQVQPLGKQRPAPCPGLRSKEKKKVNCKPKNQDEQEIPFRLREI
		MA.AG.GAAVPR...GPGSPRR..RR.Q.QPLGKQRP.P..GLRSKEKK.VNC.PKNQDE.EIPF.LREI
RetrocopyMAQAGGGAAVPRMPVGPGSPRRVQRRHQGQPLGKQRPVPWSGLRSKEKK-VNCTPKNQDEEEIPFWLREI
ParentalMRSRQEMKNPISNKKRKKAAQVTFRKTLEKEAKGVEPDIAVPKFKQRKGESDGAYMQRMQQEAQHVLFLS
		M.S.Q.MKNPI.NKKRKKAAQV.FRKTLEKEAKGVEPDIA.PKFKQRKGESD.AY.QRMQQE.QH.LFLS
RetrocopyMGSCQKMKNPIGNKKRKKAAQVAFRKTLEKEAKGVEPDIAIPKFKQRKGESD*AYIQRMQQEVQHMLFLS
ParentalKNQVPRQPEVQAAPTERSEQKKAKKAFQKRRLD---KVQRK-KEEKAADRLEQELLRDTVTFGEVVLQPP
		KNQ..RQP.VQAAP.E.SE...........R.D...K..RK.KEEK.ADRLEQELLRDT..FGEVVLQPP
RetrocopyKNQATRQPDVQAAPKEKSEKSLXXXXXXHSRSDD*IKSSRK<KEEKMADRLEQELLRDTMKFGEVVLQPP
ParentalELTVRPQRSVSKDQCCQGTEALDRLDTVGH-TXPLTASLARQRIV-GEERERAVQAYRVLKQRRRLLHGE
		ELT.RP.RS.SKDQ.......L..L...G....PLTASLA.QRIV.GEER..AVQAYR.LKQ..RLL..E
RetrocopyELTTRPGRSISKDQPGRRSQMLRMLLSFGSVSQPLTASLAYQRIV<GEER*EAVQAYRALKQ--RLLQEE
ParentalRPHLTSRKKPEPR
		RPHLTSRKK.EP.
RetrocopyRPHLTSRKKREPQ

							

							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 .00 RPM	2 .24 RPM
SRP007412_brain_prefrontal_cortex	0 .00 RPM	2 .78 RPM
SRP007412_cerebellum	0 .19 RPM	1 .42 RPM
SRP007412_heart	0 .00 RPM	1 .94 RPM
SRP007412_kidney	0 .12 RPM	2 .46 RPM
SRP007412_liver	0 .12 RPM	1 .39 RPM
SRP007412_testis	0 .15 RPM	2 .00 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_1511 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_1511 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_mmul_1511 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2661
Gorilla gorilla	retro_ggor_1857
Pongo abelii	retro_pabe_2312

Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000014878	1 retrocopy	retro_eeur_523,
Homo sapiens	ENSG00000185298	1 retrocopy	retro_hsap_2661,
Gorilla gorilla	ENSGGOG00000009333	1 retrocopy	retro_ggor_1857,
Macaca mulatta	ENSMMUG00000008831	1 retrocopy	retro_mmul_1511 ,
Monodelphis domestica	ENSMODG00000002713	1 retrocopy	retro_mdom_1355,
Mus musculus	ENSMUSG00000049957	1 retrocopy	retro_mmus_641,
Nomascus leucogenys	ENSNLEG00000013830	3 retrocopies	retro_nleu_1264, retro_nleu_1530, retro_nleu_586,
Pongo abelii	ENSPPYG00000008741	1 retrocopy	retro_pabe_2312,
Pan troglodytes	ENSPTRG00000009767	1 retrocopy	retro_ptro_1793,
Rattus norvegicus	ENSRNOG00000048712	1 retrocopy	retro_rnor_472,

	RetrogeneDB ID:	retro_mmul_1511
Retrocopy location	Organism:	*Rhesus macaque (Macaca mulatta)*
	Coordinates:	2:64127765..64128627(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	CCDC137
	Ensembl ID:	ENSMMUG00000008831
	Aliases:	None
	Description:	coiled-coil domain containing 137 [Source:HGNC Symbol;Acc:33451]

Parental	MARAGRGAAVPRAQAGPGSPRRARRRQQVQPLGKQRPAPCPGLRSKEKKKVNCKPKNQDEQEIPFRLREI
	MA.AG.GAAVPR...GPGSPRR..RR.Q.QPLGKQRP.P..GLRSKEKK.VNC.PKNQDE.EIPF.LREI
Retrocopy	MAQAGGGAAVPRMPVGPGSPRRVQRRHQGQPLGKQRPVPWSGLRSKEKK-VNCTPKNQDEEEIPFWLREI

Parental	MRSRQEMKNPISNKKRKKAAQVTFRKTLEKEAKGVEPDIAVPKFKQRKGESDGAYMQRMQQEAQHVLFLS
	M.S.Q.MKNPI.NKKRKKAAQV.FRKTLEKEAKGVEPDIA.PKFKQRKGESD.AY.QRMQQE.QH.LFLS
Retrocopy	MGSCQKMKNPIGNKKRKKAAQVAFRKTLEKEAKGVEPDIAIPKFKQRKGESD*AYIQRMQQEVQHMLFLS

Parental	KNQVPRQPEVQAAPTERSEQKKAKKAFQKRRLD---KVQRK-KEEKAADRLEQELLRDTVTFGEVVLQPP
	KNQ..RQP.VQAAP.E.SE...........R.D...K..RK.KEEK.ADRLEQELLRDT..FGEVVLQPP
Retrocopy	KNQATRQPDVQAAPKEKSEKSLXXXXXXHSRSDD*IKSSRK<KEEKMADRLEQELLRDTMKFGEVVLQPP

Parental	ELTVRPQRSVSKDQCCQGTEALDRLDTVGH-TXPLTASLARQRIV-GEERERAVQAYRVLKQRRRLLHGE
	ELT.RP.RS.SKDQ.......L..L...G....PLTASLA.QRIV.GEER..AVQAYR.LKQ..RLL..E
Retrocopy	ELTTRPGRSISKDQPGRRSQMLRMLLSFGSVSQPLTASLAYQRIV<GEER*EAVQAYRALKQ--RLLQEE

Parental	RPHLTSRKKPEPR
	RPHLTSRKK.EP.
Retrocopy	RPHLTSRKKREPQ

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

RetrogeneDB ID:

retro_mmul_1511