RetrogeneDB - Retrocopy retro_btau

                        
>retro_btau_1685
ATGGCTTTCATAACCTGGCAATTCATGCGTTCCATGTCCTCCTCCTCCACCGCCATGGCCTCGACAAAGAAAATCCTCAT

CAAGCACGTGACGGTCATCAGCGGTGGGCTGATGGGCTCCAGAATTGCCCAGGTTGCTGCAGCAACTGACCACACAGTAG

TGCTGGTGGACCAAACAGAGGACATCCTGGCAAAATCTAGAAAGGGTATCGAGGAAAGTCTTCAGAAAGTGGCCAAGAAG

AAGTCTGCAGAAAACCCAAAGAGTGCTGATAAATTTGTGGCAAAGACTCTGAGCAGCATATCACCCAGCATGGGTGCGGC

ATCCGTGGTCCACAGCACAGACCTGGTAGTGGAGGCCATTGTAGAGAATCTGCAGGTGACAAACGAGCTCTTCAAAAGGC

TAGACAAGTTTGCTGTGGAACACACAATCTTTGCCAGCAACACTTCTTCATTGCAGATCACAAGCCTAGCCAATTACACC

AAGAGACAGGACCAGTTCACTGGGCTCCATTTCTTCAACCCAGTGCCTTTGATGAAGTTTGTGGAGGTCATTAAAACACC

AATGACCAGCCAGAAGACCTTTGAATCTCTGCTAGACCTCAGCAAAGCCCTGGGAAAGCATCCTGTTGCTTGCAAGGACA

CACCTGGATTTATTATGAACCGTCTTCTGGTGCCATACCTCATAGAAGCAGTCAGGCTGTATGAATGAGGTGACATGTCC

AAGGAAGACATCGATACTGCTAAGAAGCCAGGTGCCAGGTATCCCATGGGTCCATTTGAGTGCCTCGATTATGTTGGGCT

GTATACTACAAAGTTCATCCTGGATGGTTGGCATGAAATGGATTCAAAGAACCCCCTGTTTCAGCCAGCCCATCCCTGAA

TAAGTTGGTAGCAGAGAATAAGTTTGGCAAGAAGACTGGAGATGGATATTACAAATACAAG

ORF - retro_btau_1685 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	85.08 %
Parental protein coverage:	100.0 %
Number of stop codons detected:	1
Number of frameshifts detected:	1

Retrocopy - Parental Gene Alignment:

                                ParentalMAFVTRQFVRSMSSSSSAAASAKKILVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILEKSRKGI
MAF.T.QF.RSMSSSS.A.AS.KKIL.KHVTVI.GGLMG..IAQVAAAT.HTVVLVDQTEDIL.KSRKGI
RetrocopyMAFITWQFMRSMSSSSTAMASTKKILIKHVTVISGGLMGSRIAQVAAATDHTVVLVDQTEDILAKSRKGI
ParentalEESLRKVAKKKFAENPKGADEFVAKTLSSISTSTDAASVVHSTDLVVEAIVENLQMKNELFKRLDKFAAE
EESL.KVAKKK.AENPK.AD.FVAKTLSSIS.S..AASVVHSTDLVVEAIVENLQ..NELFKRLDKFA.E
RetrocopyEESLQKVAKKKSAENPKSADKFVAKTLSSISPSMGAASVVHSTDLVVEAIVENLQVTNELFKRLDKFAVE
ParentalHTIFASNTSSLQITSLANSTTRQDRFAGLHFFNPVPLMKLVEVIKTPMTSQKTFESLLDFSRALGKHPVA
HTIFASNTSSLQITSLAN.T.RQD.F.GLHFFNPVPLMK.VEVIKTPMTSQKTFESLLD.S.ALGKHPVA
RetrocopyHTIFASNTSSLQITSLANYTKRQDQFTGLHFFNPVPLMKFVEVIKTPMTSQKTFESLLDLSKALGKHPVA
ParentalCKDTPGFIVNRLLVPYLMEAVRLCERGEASKEDIDMAMKLGAGYPMGPFELLDYVGLDTTKFILDGWHEM
CKDTPGFI.NRLLVPYL.EAVRL.E.G..SKEDID.A.K.GA.YPMGPFE.LDYVGL.TTKFILDGWHEM
RetrocopyCKDTPGFIMNRLLVPYLIEAVRLYE*GDMSKEDIDTAKKPGARYPMGPFECLDYVGLYTTKFILDGWHEM
ParentalDSKNPLFQPC-PSLNKLVAEKKFGKKSGEGFYKYK
DSKNPLFQP..PSLNKLVAE.KFGKK.G.G.YKYK
RetrocopyDSKNPLFQPA<PSLNKLVAENKFGKKTGDGYYKYK

                            

                            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 .00 RPM	183 .05 RPM
ERP005899_muscle	0 .00 RPM	183 .23 RPM
SRP017611_brain	0 .00 RPM	18 .77 RPM
SRP017611_kidney	0 .00 RPM	242 .36 RPM
SRP017611_liver	0 .00 RPM	47 .19 RPM
SRP030211_testis	0 .12 RPM	23 .45 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_1685 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1685 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_btau_1685 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002049	2 retrocopies	retro_btau_1111, retro_btau_1685 ,
Callithrix jacchus	ENSCJAG00000015938	1 retrocopy	retro_cjac_772,
Echinops telfairi	ENSETEG00000013807	1 retrocopy	retro_etel_1694,
Felis catus	ENSFCAG00000022260	1 retrocopy	retro_fcat_1225,
Homo sapiens	ENSG00000138796	1 retrocopy	retro_hsap_1571,
Gorilla gorilla	ENSGGOG00000004423	1 retrocopy	retro_ggor_1196,
Macaca mulatta	ENSMMUG00000023254	1 retrocopy	retro_mmul_2217,
Nomascus leucogenys	ENSNLEG00000012951	1 retrocopy	retro_nleu_1738,
Pongo abelii	ENSPPYG00000014986	1 retrocopy	retro_pabe_1296,
Pan troglodytes	ENSPTRG00000016351	1 retrocopy	retro_ptro_1058,

	RetrogeneDB ID:	retro_btau_1685
Retrocopy location	Organism:	*Cow (Bos taurus)*
	Coordinates:	9:94351853..94352794(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	BT.58717
	Ensembl ID:	ENSBTAG00000002049
	Aliases:	None
	Description:	hydroxyacyl-coenzyme A dehydrogenase, mitochondrial [Source:RefSeq peptide;Acc:NP_001039799]

Parental	MAFVTRQFVRSMSSSSSAAASAKKILVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILEKSRKGI
	MAF.T.QF.RSMSSSS.A.AS.KKIL.KHVTVI.GGLMG..IAQVAAAT.HTVVLVDQTEDIL.KSRKGI
Retrocopy	MAFITWQFMRSMSSSSTAMASTKKILIKHVTVISGGLMGSRIAQVAAATDHTVVLVDQTEDILAKSRKGI

Parental	EESLRKVAKKKFAENPKGADEFVAKTLSSISTSTDAASVVHSTDLVVEAIVENLQMKNELFKRLDKFAAE
	EESL.KVAKKK.AENPK.AD.FVAKTLSSIS.S..AASVVHSTDLVVEAIVENLQ..NELFKRLDKFA.E
Retrocopy	EESLQKVAKKKSAENPKSADKFVAKTLSSISPSMGAASVVHSTDLVVEAIVENLQVTNELFKRLDKFAVE

Parental	HTIFASNTSSLQITSLANSTTRQDRFAGLHFFNPVPLMKLVEVIKTPMTSQKTFESLLDFSRALGKHPVA
	HTIFASNTSSLQITSLAN.T.RQD.F.GLHFFNPVPLMK.VEVIKTPMTSQKTFESLLD.S.ALGKHPVA
Retrocopy	HTIFASNTSSLQITSLANYTKRQDQFTGLHFFNPVPLMKFVEVIKTPMTSQKTFESLLDLSKALGKHPVA

Parental	CKDTPGFIVNRLLVPYLMEAVRLCERGEASKEDIDMAMKLGAGYPMGPFELLDYVGLDTTKFILDGWHEM
	CKDTPGFI.NRLLVPYL.EAVRL.E.G..SKEDID.A.K.GA.YPMGPFE.LDYVGL.TTKFILDGWHEM
Retrocopy	CKDTPGFIMNRLLVPYLIEAVRLYE*GDMSKEDIDTAKKPGARYPMGPFECLDYVGLYTTKFILDGWHEM

Parental	DSKNPLFQPC-PSLNKLVAEKKFGKKSGEGFYKYK
	DSKNPLFQP..PSLNKLVAE.KFGKK.G.G.YKYK
Retrocopy	DSKNPLFQPA<PSLNKLVAENKFGKKTGDGYYKYK

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

RetrogeneDB ID:

retro_btau_1685