RetrogeneDB ID: retro_btau_616

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 16:29369554..29370992(+)
• Located in intron of: ENSBTAG00000016185

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: BT.64411
• Ensembl ID: ENSBTAG00000017557
• Aliases: None
• Description: glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial [Source:RefSeq peptide;Acc:NP_001039801]

Sequence

>retro_btau_616
GTTACTGTATCAGAAGAGGTGGTCTTAAAGCAAGTTGAAGAATCAGAGAAAAGATATAAGGTCACTCACTGTGGAATTTA
GATGAAATTCCTATTGCAGTAAAAGACAACTTTAGCACATCTGGCATTGAGACAACATGTGCATCAAACATACTGAAAAG
TTAAGTATCACCTTAAATTCCACAGAGGTTGTTGGATCAGGGAGCTCTGTTAATGGTAAAAACAAACTTAGATGAGTCTG
CTATGGGATACAGAAGCACAGATGGAATTTTTGGACCAGTTATAAACCCATGGAGTTATTCAAACAATATAGAGAAAAGA
GGAAGCAGAAGTCTCATGGTGAGAATAAGGATTCAAATTGGCTTATAACTGGAGGAAGCTCAGGAGGGAGTGCAGTGGCT
GTGTCAGCATTCACTTGCTTCATTGCTTTAGGACCAGATTCCAGAGGATCAACCAGCAATCCAGCTGCCCACTATGAGAT
TGTTGGTTTAAAATCCAGCTATGACTTAGTTTCTTGTCATGGCCTCATTCCCCTGGTGAATTCAATGATGTGCCCAGAAT
CTTAACTAGAGGTGTGGATGATGCACCAATGTGTTGAGTATACTAGCTGGGCAGGATTTCTAAGATTCTACCACAATTCA
AGATCCTGTTAAAACCATTTATGCTTCCCAGTTTAACAGATATGAGCAAACGATGTATAGGAATTCCAAAGGAATATCTT
ATACCAGAATTGTCAAGTGAAGTACAATCTTTTTGGTCCAAAGCTGCTAATCTCTTTGAGTCTGAGGGGGCCAAAGTAAT
TGAAGTGTCCCTGCCCCAACCAGTTTTCAATTGTCTGCTACCATGTACTGTGTACATCAGAAGTGGCATCAAATATGGCA
AGATTTGATAGGTTAGAATATGGTCACTGATTTAACATTGATGTGTCTACTGAAGCCATGTATGCTGCAACTAAACAAGA
AGAGTTCAATTATTTGGTGTGGGGAAGAATCCTCTCAGGAAACTTTCTTATTAAAAGAAAATTATGAGAACTATTTTATC
AAAGCAGAGAAAGTGAGATGACTCATTACTAATGATTTTGTGAATGTTTTTAACTCTGGAGTAGATGTTTTGCTAACTTC
CACTGCCTTGAGTGAGGCAGTGCCATACACAAAGTGCATCAAAGAAGACAACAGAACATGAATTGCCCAGGGTGATATTT
TTACACAGACTGTAATATGGCAGAATTGCCAATGGTGAGTGTCCCTACAGCCCTGTCAAGCCAAGGATTGTCAATAGGAC
TGCAGTTTAATGGTTGTACATTTTGTGACCAGCTGCTTTTTTACAGTTTGCAAATGGTTTGAAAAACAAGTACTGTTTCC
TGTTACTCAACTTATCAAACTAATGGATGATTGTTCATCAAACTGTGAAAATTAAACGTTATCTCTGCTTCTCTAAAA

Alignment

ORF - retro_btau_616 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.95 %
• Parental protein coverage: 92.4 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 13

Retrocopy - Parental Gene Alignment:

Parental  ITVSEEVALKQAEESEKRYKK-GHSLGDLDGIPIAVKDNFSTSGIETTCASNMLKGYVPP-YNATVVQKL
          .TVSEEV.LKQ..E......K.GHSL..LD.IPIAVKDNFSTSGIETTCASN.LK..V.P..N.T.V...
Retrocopy VTVSEEVVLKQV-EESEKRYK<GHSLWNLDEIPIAVKDNFSTSGIETTCASNILKS*VSP<LNSTEV---

Parental  LDQGALLMGK-TNLDEFAMGSGSTDGIFGPVKNPWSYS-KQYREKRKQNSHSENEDSNWLITGGSSGGSA
          ...G....GK.TNLDE.AMG..STDGIFGPV.NPWSYS.KQYREKRKQ.SH.EN.DSNWLITGGSSGGSA
Retrocopy VGSGSSVNGK>TNLDESAMGYRSTDGIFGPVINPWSYS<KQYREKRKQKSHGENKDSNWLITGGSSGGSA

Parental  AAVSAFTCFAALGSDTGGSTRNPAAHCGVVGLKPSYGLVSRHGLIPLVNSM-DVPGILTRCVDDA-ATVL
          .AVSAFTCF.ALG.D..GST.NPAAH...VGLK.SY.LVS.HGLIPLVNSM.DVP.ILTR.VDDA...VL
Retrocopy VAVSAFTCFIALGPDSRGSTSNPAAHYEIVGLKSSYDLVSCHGLIPLVNSM<DVPRILTRGVDDA<TNVL

Parental  GVLAGHDPKDSTTIQDPV-KPFTLPSLTDVSKLCIGIPKEYLTPELSSEVQSLWSKAANLFESEGAKVTE
          ..LAG.D..DSTTIQDPV.KPF.LPSLTD.SK.CIGIPKEYL.PELSSEVQS.WSKAANLFESEGAKV.E
Retrocopy SILAGQDF*DSTTIQDPV>KPFMLPSLTDMSKRCIGIPKEYLIPELSSEVQSFWSKAANLFESEGAKVIE

Parental  VSLPH-TSY-SIVCYHVLCTSEVASNMARFDGLEYGHRCDSDVSTEAMYAATRREGFNDVVRGRILSGNF
          VSLP..TS..SIVCYHVLCTSEVASNMARFD.LEYGH....DVSTEAMYAAT..E.FN..V.GRILSGN.
Retrocopy VSLPQ<TSF<SIVCYHVLCTSEVASNMARFDRLEYGH*FNIDVSTEAMYAATKQEEFNYLVWGRILSGN-

Parental  FLLK-ENYENYFVKAQKVRRLIANDFVNVFNSGVDVLLTPTTLSEAVPYTEFIKEDNRTRSAQDDIFTQA
          FL.K.ENYENYF.KA.KVR.LI.NDFVNVFNSGVDVLLT.T.LSEAVPYT..IKEDNRT..AQ.DIFTQ.
Retrocopy FLIK>ENYENYFIKAEKVR*LITNDFVNVFNSGVDVLLTSTALSEAVPYTKCIKEDNRT*IAQGDIFTQT

Parental  V-NMAGLPAVSVPVALSSQGLPIGLQFIGRAFCDQQL-LIVAKWFEKQVQFPVIQLQELMDDCSSVFENE
          V.NMA.LP.VSVP.ALSSQGL.IGLQF.G..FCDQ.L...V.KWFEKQV.FPV.QL..LMDDCSS..EN.
Retrocopy V<NMAELPMVSVPTALSSQGLSIGLQFNGCTFCDQLL>FTVCKWFEKQVLFPVTQLIKLMDDCSSNCEN*

Parental  KLA-SVSLK
          .L..S.SLK
Retrocopy TLS<SASLK

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
ERP005899_liver	0.00 RPM	12.98 RPM
ERP005899_muscle	0.00 RPM	20.90 RPM
SRP017611_brain	0.00 RPM	12.01 RPM
SRP017611_kidney	0.00 RPM	24.83 RPM
SRP017611_liver	0.00 RPM	9.89 RPM
SRP030211_testis	0.02 RPM	27.40 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_616 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_616 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_616 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017557	3 retrocopies	retro_btau_476, retro_btau_493, retro_btau_616 ,
Choloepus hoffmanni	ENSCHOG00000001036	1 retrocopy	retro_chof_2382,
Callithrix jacchus	ENSCJAG00000006200	4 retrocopies	retro_cjac_1421, retro_cjac_3781, retro_cjac_3919, retro_cjac_692,
Cavia porcellus	ENSCPOG00000021670	1 retrocopy	retro_cpor_179,
Homo sapiens	ENSG00000130348	3 retrocopies	retro_hsap_1321, retro_hsap_466, retro_hsap_514,
Gorilla gorilla	ENSGGOG00000008261	3 retrocopies	retro_ggor_1031, retro_ggor_445, retro_ggor_474,
Macaca mulatta	ENSMMUG00000008330	2 retrocopies	retro_mmul_429, retro_mmul_675,
Nomascus leucogenys	ENSNLEG00000013383	2 retrocopies	retro_nleu_1403, retro_nleu_1550,
Pongo abelii	ENSPPYG00000016883	3 retrocopies	retro_pabe_1100, retro_pabe_230, retro_pabe_268,
Pan troglodytes	ENSPTRG00000018462	2 retrocopies	retro_ptro_351, retro_ptro_902,