RetrogeneDB - Retrocopy retro_btau

						
>retro_btau_1358
ACATGGCTCGCTCTTGTCGAACGGGGAGGCTGTACCTTCACCCAGAAGATCAAGGTGGCGGTGGAGAATGGAGCCAGTGG

AGTGATCATCTATAACTTTCCAGGAACTGGCAATCAGGTCTTTCCCATGTCTCATCAGATATTTGAAGACATCGTTGTGG

TGATGATTGGTAACTTAAAAGGCATGGAGATTTTGCATTTAATTCAGAAGGGTGTTCATGTGACCGTCACGATTGAGGTG

GGAAGAAAACACATCATCTGGATGAATCACTATTTTGTCTCTTTTGTGATCGTCACAACCGCTACGTTAGTGTATTTCAT

CTTTTATCATATTCGAAGACTTTGGGTAGCAAGGGTTCAGAACCGGAGGTGGCAGCGGTTAACAAATGATCTCAAGAAAG

CATTTGGCCAGCTTCAGGTTCGGGTACTGAAAGAGGGGGACGAGGAAGTAAGCGGCAATGGAGATAGCTGCGTAGTTTGC

TTTGAACTCTATAAGCCTAACGATACAATTCGTGTTCTGACCTGTAAACATTTTTTCCACAAGAATTGCATTGACCCCTG

GATCTTAGCCCATGGGACATGCCCCATGTGCAAATGTGATATTCTTAAAGCTTTGGGGATTCAGATGGATGTTGAAGATG

GAACAGAGTCTTTGCAAGTTTTAATGTCCAACGAATTGGCTGATATCCTGTCATCTAGTGAAGAGGGCACAAATAATGAA

CTTCCTCCTTCAGGA

ORF - retro_btau_1358 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	59.36 %
Parental protein coverage:	58.24 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalSWLALIQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAGDIVAIMIGNLKGTKILQSIQ
		.WLAL..RGG.CTF..KI..A.E.GASG..I.NFPGT.N.V.PMSH....DIV..MIGNLKG..IL..IQ
RetrocopyTWLALVERGG-CTFTQKIKVAVENGASGVIIYNFPGTGNQVFPMSHQIFEDIVVVMIGNLKGMEILHLIQ
ParentalRGIQVTMVIEVGKKHGPWVNHYSIFFVSVSFFIITAATVGYFIFYSARRLRNARAQSRKQRQLKADAKKA
		.G..VT..IEVG.KH..W.NHY...FV.V.....TA..V.YFIFY..RRL..AR.Q.R....L..D.KKA
RetrocopyKGVHVTVTIEVGRKHIIWMNHYFVSFVIVT----TATLV-YFIFYHIRRLWVARVQNRRWQRLTNDLKKA
ParentalIGRLQLRTLKQGDKEIGPDGDSCAVCIELYKPNDLVRILTCNHVFHKTCVDPWLLEHRTCPMCKCDILKA
		.G.LQ.R.LK.GD.E....GDSC.VC.ELYKPND..R.LTC.H.FHK.C.DPW.L.H.TCPMCKCDILKA
RetrocopyFGQLQVRVLKEGDEEVSGNGDSCVVCFELYKPNDTIRVLTCKHFFHKNCIDPWILAHGTCPMCKCDILKA
ParentalLGIEVDVEDGSVSLQVPVSNETSSNASPHEEDNRSETASSG
		LGI..DVEDG..SLQV..SNE.....S..EE....E...SG
RetrocopyLGIQMDVEDGTESLQVLMSNELADILSSSEEGTNNELPPSG

							

							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
ERP005899_liver	0 .29 RPM	692 .77 RPM
ERP005899_muscle	0 .16 RPM	139 .26 RPM
SRP017611_brain	0 .00 RPM	17 .91 RPM
SRP017611_kidney	0 .06 RPM	133 .84 RPM
SRP017611_liver	0 .00 RPM	190 .73 RPM
SRP030211_testis	38 .18 RPM	10 .97 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_1358 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1358 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_btau_1358 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2651
Oryctolagus cuniculus	retro_ocun_37
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	ENSBTAG00000004913	1 retrocopy	retro_btau_217,
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,
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_btau_1358
Retrocopy location	Organism:	*Cow (Bos taurus)*
	Coordinates:	4:87914161..87914896(-)
	Located in intron of:	ENSBTAG00000005110
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	BT.29416
	Ensembl ID:	ENSBTAG00000022920
	Aliases:	None
	Description:	E3 ubiquitin-protein ligase RNF128 precursor [Source:RefSeq peptide;Acc:NP_001069539]

Parental	SWLALIQRGGGCTFADKIHLAYERGASGAVIFNFPGTRNEVIPMSHPGAGDIVAIMIGNLKGTKILQSIQ
	.WLAL..RGG.CTF..KI..A.E.GASG..I.NFPGT.N.V.PMSH....DIV..MIGNLKG..IL..IQ
Retrocopy	TWLALVERGG-CTFTQKIKVAVENGASGVIIYNFPGTGNQVFPMSHQIFEDIVVVMIGNLKGMEILHLIQ

Parental	RGIQVTMVIEVGKKHGPWVNHYSIFFVSVSFFIITAATVGYFIFYSARRLRNARAQSRKQRQLKADAKKA
	.G..VT..IEVG.KH..W.NHY...FV.V.....TA..V.YFIFY..RRL..AR.Q.R....L..D.KKA
Retrocopy	KGVHVTVTIEVGRKHIIWMNHYFVSFVIVT----TATLV-YFIFYHIRRLWVARVQNRRWQRLTNDLKKA

Parental	IGRLQLRTLKQGDKEIGPDGDSCAVCIELYKPNDLVRILTCNHVFHKTCVDPWLLEHRTCPMCKCDILKA
	.G.LQ.R.LK.GD.E....GDSC.VC.ELYKPND..R.LTC.H.FHK.C.DPW.L.H.TCPMCKCDILKA
Retrocopy	FGQLQVRVLKEGDEEVSGNGDSCVVCFELYKPNDTIRVLTCKHFFHKNCIDPWILAHGTCPMCKCDILKA

Parental	LGIEVDVEDGSVSLQVPVSNETSSNASPHEEDNRSETASSG
	LGI..DVEDG..SLQV..SNE.....S..EE....E...SG
Retrocopy	LGIQMDVEDGTESLQVLMSNELADILSSSEEGTNNELPPSG

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

RetrogeneDB ID:

retro_btau_1358