RetrogeneDB ID: retro_btau_1658

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:78566943..78567499(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSAT1
• Ensembl ID: ENSBTAG00000013960
• Aliases: None
• Description: phosphoserine aminotransferase [Source:RefSeq peptide;Acc:NP_001095620]

Sequence

>retro_btau_1658
GGTTGGATGAGCCAGTTCCATGCTATCCCCTTAAGCTTGATTGACCTGAAAGTAGGGAGGTGTGCCAGCCATTCGATGGC
AAAAGCTTGGTCACCTAAGGCCCCAGAAGCCTTGAAGTTTGGGAACTGTGAATGTTATCCATTCTAAACTTAGAAGTTAC
AGGAAAATTCTGAATCCAAGACCCTGGAACCTCAATCAGGTCACCACTGCATGTATTACTGCACAAATGAGACCAGGCCC
AGAGCAGAATTTTGCTTTGTTCCTGATGTCAAAGGAGCAGTGGCTGCTTTTTGACATGTCCTCAAATTTCCCATATAAAC
CAGTTTGATGTTTAAAAGTTTGGTGTGATTTTTGATGGTGCCCAGAAGAATGCTGGCTCTGTAGGGGTCACGATGGTGAT
ATTTCAAGATATCCTGCTAGGGTTTGCCCTCAGAGAGTGCCCTTCCCTTGTGGAATACAAAGTGCAGGCCGGAAACAACA
CTTTATTCAACACAACTCCCTTCCTTGTTTCTACAGCATCAGCTTGGTCTTGGAGTAGATCAAGAATAACAGTGGC

Alignment

ORF - retro_btau_1658 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.21 %
• Parental protein coverage: 50.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GGCGQFSAVPLNLIGLKAGRCADYVVTGSWSAKAAEEAKKFG-TVNIVHPKLGSYTKIPDPSTWTLNPDA
          G...QF.A.PL.LI.LK.GRCA.......WS.KA.E.A.KFG.TVN..H.KL.SY.KI..P..W.LN...
Retrocopy GWMSQFHAIPLSLIDLKVGRCASHSMAKAWSPKAPE-ALKFG>TVNVIHSKLRSYRKILNPRPWNLNQVT

Parental  SY-VYYCANETVHGVEFDFIPDVKGAV-LVCDMSSNFLSRPV-DVSKFGVIFAGAQKNVGSAGVTVVIIR
          ....YYC.NET....EF.F.PDVKGAV.L..DMSSNF...PV.DV.KFGVIF.GAQKN.GS.GVT.VI..
Retrocopy TA<MYYCTNETRPRAEFCFVPDVKGAV>LLFDMSSNFPYKPV>DV*KFGVIFDGAQKNAGSVGVTMVIFQ

Parental  DDLLGFALKECPSVLDYKVQAGNNSLYNTPPCF-SIYVMGLVLEWIKNNGG
          D.LLGFAL.ECPS...YKVQAGNN.L.NT.P.....Y...LVLE.IKNN.G
Retrocopy DILLGFALRECPSLVEYKVQAGNNTLFNTTPFL<CFYSISLVLE*IKNNSG

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	336.83 RPM
ERP005899_muscle	0.00 RPM	10.72 RPM
SRP017611_brain	0.00 RPM	46.09 RPM
SRP017611_kidney	0.00 RPM	62.71 RPM
SRP017611_liver	0.00 RPM	48.93 RPM
SRP030211_testis	0.04 RPM	27.83 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1658 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1658 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1658 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006898	1 retrocopy	retro_amel_375,
Bos taurus	ENSBTAG00000013960	1 retrocopy	retro_btau_1658 ,
Canis familiaris	ENSCAFG00000001570	1 retrocopy	retro_cfam_269,
Choloepus hoffmanni	ENSCHOG00000003817	1 retrocopy	retro_chof_2702,
Callithrix jacchus	ENSCJAG00000003319	1 retrocopy	retro_cjac_1203,
Echinops telfairi	ENSETEG00000004158	1 retrocopy	retro_etel_99,
Homo sapiens	ENSG00000135069	3 retrocopies	retro_hsap_2267, retro_hsap_4054, retro_hsap_412,
Gorilla gorilla	ENSGGOG00000015480	1 retrocopy	retro_ggor_407,
Loxodonta africana	ENSLAFG00000017917	2 retrocopies	retro_lafr_1249, retro_lafr_660,
Macaca mulatta	ENSMMUG00000011868	2 retrocopies	retro_mmul_1029, retro_mmul_2341,
Mustela putorius furo	ENSMPUG00000012566	1 retrocopy	retro_mputfur_808,
Nomascus leucogenys	ENSNLEG00000002989	3 retrocopies	retro_nleu_1010, retro_nleu_1288, retro_nleu_2805,
Oryctolagus cuniculus	ENSOCUG00000007765	1 retrocopy	retro_ocun_1092,
Pongo abelii	ENSPPYG00000019313	3 retrocopies	retro_pabe_1950, retro_pabe_308, retro_pabe_3328,
Pan troglodytes	ENSPTRG00000021045	2 retrocopies	retro_ptro_1606, retro_ptro_316,
Rattus norvegicus	ENSRNOG00000013971	1 retrocopy	retro_rnor_1663,
Tupaia belangeri	ENSTBEG00000012946	1 retrocopy	retro_tbel_1577,
Tarsius syrichta	ENSTSYG00000000093	2 retrocopies	retro_tsyr_1073, retro_tsyr_1212,