RetrogeneDB - Retrocopy retro_ocun

                        
>retro_ocun_37
ATGACTCTACTCAAGAATGGCACTTGGAGAAACAACACTGCATCTTCCTGGCTTCTGAAGTTCACTTTTCTTTGGCTGTT

TAGTCAGTACTCTTGCACAACAAGTGCTGTTTGGACTGCATACATGAACATATCATTTCATGTTGGGAATCGCATGTTGT

CAGAGTTGGGGGAGACTGGAGTATTTGGAAGGGGCTCTGCTTTGAAGAGAGTGACAGGAGTTATAGTGCCACCAGAGGGA

AAAACCCAAAATGCATGTAATCCTACTACCAGTTTCAGCAGAACAAAGAACTCAGAGACATGGCTAGCACTTATTGAACG

GGGAGGTTGTACTTTCACACAGAAAATCAAGGTGGCGACTGAGAAGGGAGCCAGTGGAGTGATCATCTATAACTTTCCAG

GAACTGGCAATCAGGTTTTCCCCATGACTCATCAGGCATTTGAAGGCATTGTTGTGGTTATGATTGGTAACTTAAAAGGT

ATGGAAATTTTGCATTTAATTCAGAAGGGAGTTCATGTAACAGTCATGGTTGATGTGGGGAGAAAACACATCATCTGGAT

GAATCATTATTTTGTCTCTTTTATGATCGTCACAACTGCTACCTTAGCATATTTCGTTTTTTATCATATTCGAAGACTTT

GGATAGCAAGGATTCAGAATAGGAGATGGCAGCGATTAACAACAGATATCAAGAGAGCATTTGGACAACTTCAACTTCGG

GTATTAAAAGAGGGAGATGAGGAAATAACTCCAAATGGCGATAGCTGCGTAGTTTGCTTTGAACTCTATAAGCCTAATGA

TATAGTTCGTATTCTGACTTGTAAACACTTTTTCCACAAGAATTGCATTGACCCCTGGATTCTAGCCCATGGGACATGCC

CCATGTGCAAGTGTGACATTCTTAAAGCTTTGGGAATTCAAGTGGATATTGAAGATGGAACTGAATCTTTACAAGTCCTG

ATGTCAAGTGAATTGCCTGAAATCCTGTCACCTAGAGAAGAGGAGGCAGATAATGAACCTCCTCCTGCAAGGATATCAGA

TAAAGCAACCCACGTGGAGGAGAACCCGACTTCTCAGAATGATGACCGCCAGGCTGATTTAGTTGTGGAAAACGTTCATC

CTTCAACC

ORF - retro_ocun_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	56.91 %
Parental protein coverage:	57.48 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalSWLALIQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAGDIVAIMIGNLKGTKILQWIQ
.WLALI.RGG.CTF..KI..A.E.GASG..I.NFPGT.N.V.PM.H.....IV..MIGNLKG..IL..IQ
RetrocopyTWLALIERGG-CTFTQKIKVATEKGASGVIIYNFPGTGNQVFPMTHQAFEGIVVVMIGNLKGMEILHLIQ
ParentalSGIQVTMVIEVGKKHGPWVNHYSIFFVSVSFFIITAATVGYFIFYSARRLRNARAQSRKQRQLKADAKKA
.G..VT....VG.KH..W.NHY...F..V.....TA...........R.L..AR.Q.R....L..D.K.A
RetrocopyKGVHVTVMVDVGRKHIIWMNHYFVSFMIVT----TATLAYFVFYHIRR-LWIARIQNRRWQRLTTDIKRA
ParentalIGRLQLRTLKQGDKEIGPDGDSCAVCIELYKPNDLVRILTCNHIFHKTCVDPWLLEHRTCPMCKCDILKA
.G.LQLR.LK.GD.EI.P.GDSC.VC.ELYKPND.VRILTC.H.FHK.C.DPW.L.H.TCPMCKCDILKA
RetrocopyFGQLQLRVLKEGDEEITPNGDSCVVCFELYKPNDIVRILTCKHFFHKNCIDPWILAHGTCPMCKCDILKA
ParentalLGIEVDVEDGSVSLQVPVSNETSHSASPHEEDNRSE
LGI.VD.EDG..SLQV..S.E.....SP.EE....E
RetrocopyLGIQVDIEDGTESLQVLMSSELPEILSPREEEADNE

                            

                            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
SRP017611_brain	0 .55 RPM	15 .45 RPM
SRP017611_kidney	0 .10 RPM	62 .54 RPM
SRP017611_liver	0 .08 RPM	47 .09 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_37 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_37 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ocun_37 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2651
Bos taurus	retro_btau_1358
Sus scrofa	retro_sscr_597

Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000022920	1 retrocopy	retro_btau_1358,
Loxodonta africana	ENSLAFG00000002816	1 retrocopy	retro_lafr_946,
Macropus eugenii	ENSMEUG00000001567	1 retrocopy	retro_meug_1139,
Mustela putorius furo	ENSMPUG00000003695	1 retrocopy	retro_mputfur_340,
Oryctolagus cuniculus	ENSOCUG00000012328	1 retrocopy	retro_ocun_37 ,
Pelodiscus sinensis	ENSPSIG00000010727	1 retrocopy	retro_psin_49,
Pan troglodytes	ENSPTRG00000022151	1 retrocopy	retro_ptro_2651,
Sus scrofa	ENSSSCG00000012551	1 retrocopy	retro_sscr_597,
Ictidomys tridecemlineatus	ENSSTOG00000022922	2 retrocopies	retro_itri_1254, retro_itri_1255,
Tursiops truncatus	ENSTTRG00000007536	1 retrocopy	retro_ttru_6,

	RetrogeneDB ID:	retro_ocun_37
Retrocopy location	Organism:	*Rabbit (Oryctolagus cuniculus)*
	Coordinates:	7:21975921..21977049(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSOCUG00000024828
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	RNF128
	Ensembl ID:	ENSOCUG00000012328
	Aliases:	None
	Description:	ring finger protein 128, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:21153]

Parental	SWLALIQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAGDIVAIMIGNLKGTKILQWIQ
	.WLALI.RGG.CTF..KI..A.E.GASG..I.NFPGT.N.V.PM.H.....IV..MIGNLKG..IL..IQ
Retrocopy	TWLALIERGG-CTFTQKIKVATEKGASGVIIYNFPGTGNQVFPMTHQAFEGIVVVMIGNLKGMEILHLIQ

Parental	SGIQVTMVIEVGKKHGPWVNHYSIFFVSVSFFIITAATVGYFIFYSARRLRNARAQSRKQRQLKADAKKA
	.G..VT....VG.KH..W.NHY...F..V.....TA...........R.L..AR.Q.R....L..D.K.A
Retrocopy	KGVHVTVMVDVGRKHIIWMNHYFVSFMIVT----TATLAYFVFYHIRR-LWIARIQNRRWQRLTTDIKRA

Parental	IGRLQLRTLKQGDKEIGPDGDSCAVCIELYKPNDLVRILTCNHIFHKTCVDPWLLEHRTCPMCKCDILKA
	.G.LQLR.LK.GD.EI.P.GDSC.VC.ELYKPND.VRILTC.H.FHK.C.DPW.L.H.TCPMCKCDILKA
Retrocopy	FGQLQLRVLKEGDEEITPNGDSCVVCFELYKPNDIVRILTCKHFFHKNCIDPWILAHGTCPMCKCDILKA

Parental	LGIEVDVEDGSVSLQVPVSNETSHSASPHEEDNRSE
	LGI.VD.EDG..SLQV..S.E.....SP.EE....E
Retrocopy	LGIQVDIEDGTESLQVLMSSELPEILSPREEEADNE

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

RetrogeneDB ID:

retro_ocun_37