RetrogeneDB ID: retro_btau_476

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:70952500..70953414(+)
• Located in intron of: None

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_476
CTCATTCCCCTGGTGAATTCAATGATGTGCCCAGAATCTTAACTAGATGCATGGATGATGCACCATTGTGTTGAGTATAC
TAGCTGGGCAGGATCTCTAAGATTCTACCAAAATTCAAGATCCTGTTAAAATCATTTATGCTTCCCAGTTTAACAGATGT
GAGCAAATGATGTATAGGAATTCCAAAGGAATATCTTATACCAGAATTGTCAAGTGAAGTACAATCTCTTTGGTCCAAAG
CTGCTAATCTCTTTGAGTCTGAGGGGGCCAAAGTAAATGAAGTGTCCCTGCCCCAACCAGTTATTCAGTTGTCTGCTACC
ATGTACTGTGTACATCAGAACTGGCATCAAATATGGCAAGATTTGATAGGTTAGAATATGGTCACTGATTTGACATTGAT
GTGTCTACTGAAGCCATGTATGCTGCAACTAAACAAGAAGAGTTCAATGATTTGGTGTGGGGAAGAATCCTCTCAGGAAA
CTTTATTAAAAGAAAATTATGAGAACTATTTTATCAAAGCAGAGAAAGTGAGAGGACTCATTACTAATGATTTTGTGAAT
GTTTTTAACTCTGGAGTAAATGTTTTCCTAACTTTTACTACCTTGAGTGAGGCAGTGCCATACACAAAGTGCATCAAAGA
AGACAACAGAACATGAATTGCCCAGGGTGATATTTTTACACAGACTGTAAATTTGGCAGAATTCCCAGTGGTGACTGTCC
CTACAGCCCTGCCAAGCCAAGGACTGTCAATAGAACTGCAGTTTAATGGTTGTGCATTCTGTGACCAGCTGCTTTTTTAC
AGTCTGTAAATGGTTTGAAAAGCAAGTACAGTTTACTGTTACTCAACTTCTCAAACTAATGGATGATTGTTGATCAAACT
TTGAAAATTAAACATTATCTCTGCTTCTCTAAAA

Alignment

ORF - retro_btau_476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.93 %
• Parental protein coverage: 58.37 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  LIPLVNSM-DVPGILTRCVDDA-ATVLGVLAGHDPKDSTTIQDPVK-PFTLPSLTDVSKLCIGIPKEYLT
          LIPLVNSM.DVP.ILTRC.DDA...VL..LAG.D..DST.IQDPVK..F.LPSLTDVSK.CIGIPKEYL.
Retrocopy LIPLVNSM<DVPRILTRCMDDA<TIVLSILAGQDL*DSTKIQDPVK>SFMLPSLTDVSK*CIGIPKEYLI

Parental  PELSSEVQSLWSKAANLFESEGAKVTEVSLPH-TSYSIVCYHVLCTSEVASNMARFDGLEYGHRCDSDVS
          PELSSEVQSLWSKAANLFESEGAKV.EVSLP..TSYS.VCYHVLCTSE.ASNMARFD.LEYGH..D.DVS
Retrocopy PELSSEVQSLWSKAANLFESEGAKVNEVSLPQ<TSYSVVCYHVLCTSELASNMARFDRLEYGH*FDIDVS

Parental  TEAMYAATRREGFNDVVRGRILSGNFFLLKENYENYFVKAQKVRR-LIANDFVNVFNSGVDVLLTPTTLS
          TEAMYAAT..E.FND.V.GRILSGNF...K......F.......R.LI.NDFVNVFNSGV.V.LT.TTLS
Retrocopy TEAMYAATKQEEFNDLVWGRILSGNF--IKRKL*ELFYQSRESER>LITNDFVNVFNSGVNVFLTFTTLS

Parental  EAVPYTEFIKEDNRTRSAQDDIFTQAVNMAGLPAVSVPVALSSQGLPIGLQFIGRAFCDQQL-LIVAKWF
          EAVPYT..IKEDNRT..AQ.DIFTQ.VN.A..P.V.VP.AL.SQGL.I.LQF.G.AFCDQ.L...V.KWF
Retrocopy EAVPYTKCIKEDNRT*IAQGDIFTQTVNLAEFPVVTVPTALPSQGLSIELQFNGCAFCDQLL>FTVCKWF

Parental  EKQVQFPVIQLQELMDDCSSVFENEKLA-SVSLK
          EKQVQF.V.QL..LMDDC.S.FEN..L..S.SLK
Retrocopy EKQVQFTVTQLLKLMDDC*SNFEN*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	0.00 RPM	27.40 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_476 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_476 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_476 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,