RetrogeneDB ID: retro_btau_217

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 20:55661195..55662245(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000012971
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RNF167
• Ensembl ID: ENSBTAG00000004913
• Aliases: None
• Description: E3 ubiquitin-protein ligase RNF167 [Source:RefSeq peptide;Acc:NP_001069873]

Sequence

>retro_btau_217
ATGCCCCCTACAGCCCTCTGTCTTCCTGTGGTCGTGGCCACTCTGCTGTGGGGAGCGTCCCCTGTCAGGGGACTCATTCG
AGCGACTTCTGACCACAATGGCAGCATGGAATTTGCAGACCTCCCAGCTCTCTTTGGGGCTGCCTTGAGTCCGGAAGGAC
TTAAGGGGTTTCTCGTGGAGGCTCAGCCAGCCAACGCTTGCAGCCCCATTGCCCCACCTCCCCCAGCCCAGGCCAACGGA
TCAGTTTTCATTGCATTGCTTCGAAGATTCGACTGCAAATTTGACCTCAAGGTCCTACATGCTCAGAAGGCCGGGTATGG
TGCAGCCGTGGTACACAATGTGAATTCCAATGAACTGCTGAACATGGTGGGGAGTAACGAAGAAGTCCAGCAGCAGATCT
GGATCCCTTCTGTGTTCATCAGCGAAAAGAGCTCTCAGTACCTGCGTGCCTTCTTCATCTACCAGCAGGGAGCTCAGGTG
CTTCTGGTCCCTGACAATGGATTCCTCTCCACCTATTTTTTCATCCTTTTCTATGGGATTTTGGCAATGCTCATTTTGGG
CACGGGAGCCATAGTGATAGTTCATTGGATCCATTTCCAGAAACAGCGCTGGCGGAATCTGCTGACCAAAGAGCAACTGA
AACAGATTCCTACCCACGACTATCGCAGGGGAGACCGGTATGATGTGTGTGCCATCTGCCTGGACGAATATGAGGACGGG
GATAAGTTGAGGGTCCTCCCCTGTGCTCATGCCTATCACTGCCGCTGTGTGGACCCATGGCTCACTCAGACCAAGAAGAC
GTGCCCTATTTGTAAGCAGCCTGTTTGCCGGAATCTTGGGGAGGAGGAGCAGGAGGAAGGAACTCAGGTGCAAATGGGCC
ATGAGGAAGGGGGCCTGAGAAGCCGCCCTGCCTCAGAGCGGACCTCACTTCTGGGCTCCAGCACCGTACTTCCCACTAAC
TTTGGCTCCTTAGCCCCGGCCCCCTTTGTGTTTCTTGGGTCTTCAACAGATCCCTCACACTCTCCATCCTCCTCTTCCTC
TTCCGCTGTC

Alignment

ORF - retro_btau_217 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.97 %
• Parental protein coverage: 98.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QGFLVEAHPDNACSPIAPPPPAPVNGSVFIALLRRFDCNFDLKVLNAQKAGYGAAVVHNVNSNELLNMVW
          .GFLVEA.P.NACSPIAPPPPA..NGSVFIALLRRFDC.FDLKVL.AQKAGYGAAVVHNVNSNELLNMV.
Retrocopy KGFLVEAQPANACSPIAPPPPAQANGSVFIALLRRFDCKFDLKVLHAQKAGYGAAVVHNVNSNELLNMVG

Parental  NSEEIQQQIWIPSVFIGERSSEYLRALFVYEKGARVLLVPDNSFPLGYYLIPFTGIVGLLVLAMGAVMIV
          ..EE.QQQIWIPSVFI.E.SS.YLRA.F.Y..GA.VLLVPDN.F...Y..I.F.GI...L.L..GA..IV
Retrocopy SNEEVQQQIWIPSVFISEKSSQYLRAFFIYQQGAQVLLVPDNGFLSTYFFILFYGILAMLILGTGAIVIV

Parental  RCIQHRKRLQRNRLTKEQLKQIPTHDYQKGDQYDVCAICLDEYEDGDKLRVLPCAHAYHSRCVDPWLTQT
          ..I...K...RN.LTKEQLKQIPTHDY..GD.YDVCAICLDEYEDGDKLRVLPCAHAYH.RCVDPWLTQT
Retrocopy HWIHFQKQRWRNLLTKEQLKQIPTHDYRRGDRYDVCAICLDEYEDGDKLRVLPCAHAYHCRCVDPWLTQT

Parental  RKTCPICKQPVHRGPGDDEQEEESQGQEGDEEGEPRDQPASERTPLLGSSPTPPSSFGSIAPAPLVFPGS
          .KTCPICKQPV.R..G..EQEE..Q.Q.G.EEG..R..PASERT.LLGSS...P..FGS.APAP.VF.GS
Retrocopy KKTCPICKQPVCRNLGEEEQEEGTQVQMGHEEGGLRSRPASERTSLLGSSTVLPTNFGSLAPAPFVFLGS

Parental  STDPSPSTSSAA
          STDPS.S.SS..
Retrocopy STDPSHSPSSSS

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	26.39 RPM
ERP005899_muscle	0.00 RPM	45.87 RPM
SRP017611_brain	0.00 RPM	19.60 RPM
SRP017611_kidney	0.00 RPM	39.59 RPM
SRP017611_liver	0.00 RPM	36.32 RPM
SRP030211_testis	11.14 RPM	18.33 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_217 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_217 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006392	1 retrocopy	retro_amel_43,
Bos taurus	ENSBTAG00000004913	1 retrocopy	retro_btau_217 ,
Bos taurus	ENSBTAG00000022920	1 retrocopy	retro_btau_1358,
Canis familiaris	ENSCAFG00000015830	2 retrocopies	retro_cfam_1053, retro_cfam_84,
Dipodomys ordii	ENSDORG00000011757	2 retrocopies	retro_dord_277, retro_dord_432,
Equus caballus	ENSECAG00000021567	1 retrocopy	retro_ecab_583,
Felis catus	ENSFCAG00000011173	1 retrocopy	retro_fcat_99,
Mustela putorius furo	ENSMPUG00000010940	1 retrocopy	retro_mputfur_95,
Pteropus vampyrus	ENSPVAG00000003781	1 retrocopy	retro_pvam_1206,
Sorex araneus	ENSSARG00000011216	1 retrocopy	retro_sara_517,
Sus scrofa	ENSSSCG00000017906	1 retrocopy	retro_sscr_518,
Tursiops truncatus	ENSTTRG00000001298	1 retrocopy	retro_ttru_1062,