RetrogeneDB ID: retro_btau_1245

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:108534972..108535457(+)
• Located in intron of: ENSBTAG00000002306

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRA2B
• Ensembl ID: ENSBTAG00000001697
• Aliases: TRA2B, SFRS10
• Description: Transformer-2 protein homolog beta [Source:UniProtKB/Swiss-Prot;Acc:Q3ZBT6]

Sequence

>retro_btau_1245
GTATTTGGATTGAACCTGCACACTACAGACAGAGGTCTAAAGGAAGTGTTCTCTAAATATGGCCCAATGGCTGACATGTC
TATTGCATTATGACCAGCAGTCTAGATGTTCAGGTTTGTATACTTTGAAAATGTAGATGATGCCAAGGAAGCAAAAGAGT
GTGCCAATGGAATGGAGCTTGATGAACATAGGATCAGAGTTGATTACTCTATAGCAAAAAGACCACATAATCCTACACCA
GGAATCTACAAGGGGAGATCTACCTACAGCAGCTCATGCCGTCAAGATTTTACAACAGAGGATATGATTGAGGCTATGAT
GTTCAGGACTGTCATAGTGGATCTTACAAAGGAAGTGAAGGAGGAGGATGGGGAACTGCTCAAGACAGGGATCAGACCTG
CAGAAGACAGTCACCTTCTCCCTACTGTAGTTGTGGAGGATACAGATCACACTCTAGAGCTCAATCATATTCACCTCACT
GCTAT

Alignment

ORF - retro_btau_1245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.53 %
• Parental protein coverage: 57.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VFGLSLYTTERDLREVFSKYGPIADVSIV-YDQQSRRS-RGFAFVYFENVDDAKEAKERANGMELDGRRI
          VFGL.L.TT.R.L.EVFSKYGP.AD.SI..YDQQSR.S.R...F........AKE....ANGMELD..RI
Retrocopy VFGLNLHTTDRGLKEVFSKYGPMADMSIA>YDQQSRCS<RFVYFENVDDAKEAKEC---ANGMELDEHRI

Parental  RVDFSITKRPHTPTPGIYMGRPTYGSSRRRD-YYDRGYDRGYDDRDYYSRSYRGGGGGGGGWRAAQDRDQ
          RVD.SI.KRPH.PTPGIY.GR.TY.SS.R.D..Y.RGYD.GYD..D..S.SY...G..GGGW..AQDRDQ
Retrocopy RVDYSIAKRPHNPTPGIYKGRSTYSSSCRQD<FYNRGYD*GYDVQDCHSGSYK--GSEGGGWGTAQDRDQ

Parental  IYRRRSPSPYYSRGGYRSRSRSRSYSPRRY
          ..RR.SPSPY.S.GGYRS.SR..SYSP..Y
Retrocopy TCRRQSPSPYCSCGGYRSHSRAQSYSPHCY

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	0.07 RPM	81.25 RPM
ERP005899_muscle	0.21 RPM	87.15 RPM
SRP017611_brain	0.00 RPM	42.94 RPM
SRP017611_kidney	0.36 RPM	69.70 RPM
SRP017611_liver	0.15 RPM	40.70 RPM
SRP030211_testis	0.06 RPM	123.47 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1245 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1245 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1245 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001697	2 retrocopies	retro_btau_1245 , retro_btau_850,
Bos taurus	ENSBTAG00000013308	1 retrocopy	retro_btau_36,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144,
Myotis lucifugus	ENSMLUG00000005781	2 retrocopies	retro_mluc_2565, retro_mluc_2567,
Mustela putorius furo	ENSMPUG00000003157	1 retrocopy	retro_mputfur_673,
Mus musculus	ENSMUSG00000022858	6 retrocopies	retro_mmus_1187, retro_mmus_2253, retro_mmus_2313, retro_mmus_3139, retro_mmus_3617, retro_mmus_756,
Ochotona princeps	ENSOPRG00000007990	2 retrocopies	retro_opri_24, retro_opri_930,
Rattus norvegicus	ENSRNOG00000001783	4 retrocopies	retro_rnor_1130, retro_rnor_1915, retro_rnor_2156, retro_rnor_2807,
Tarsius syrichta	ENSTSYG00000000388	1 retrocopy	retro_tsyr_1632,