RetrogeneDB ID: retro_btau_1333

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:101019787..101021510(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000031458
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.52586
• Ensembl ID: ENSBTAG00000009854
• Aliases: None
• Description: U3 small nucleolar ribonucleoprotein protein MPP10 [Source:RefSeq peptide;Acc:NP_001039782]

Sequence

>retro_btau_1333
ATGGCCCGGCCAGCCTGGCGTTGGCGGACCCTGGAGCGGTGCCTGAGGGAGGTCGGTAAAGCCACTGACAGCCCAGAGTG
CTTCCTCACCATTCAAGATGAACTGGCATCAAAGTATACTTCTTTAACAAAAGTACTTTATGACTTTAATAAAGTACTAG
AGAATGACAGGAAACATGGGAGTCCTTTAGAAAAATTGATGATAAATAATTTCGATGATGAGCAGATTTGGCAACAGTTG
GAACTGCAAAATGAACCAATTTTACAGCACTTCCAGAGTGCAGTTAGTGAAACCATTGAAGATGAAGACATCAGTCTTCT
CCCAGAGAGTGAAGAGCAGGAGTGTGAAGAGGATATGATGGAGCTGGAGGCTGCTGGCCAGGAGGACCTGGAACAAGATT
TAGAGGAGGAGGAGGTGGAGGAAGCAGAGGAGGTGGAAGTGTCAGACCTGAGTGGTGATGATCCTGAAGCAGATGAGAGA
GCCAAAAACTCAAGCAAATTGGATCTGAGGAAAAGCCCAGATTTCAGCGATGAGGACTCTGATCTTGATTTTGATATCAG
CAAACTGGAACGTCAGAGCAAGGTGTAAAGCAGAGTGCCTAGGAAACCAACAAGTAGATGATAAATTCTTCAAGCTCTCT
GAGATGGAGACCTTTTTAGAAAACATGGAAAAAGAAGAGGAACAAAGAGATGACCAAGAGGAAGATGATATTGATTTTTT
TGAAGATGTGGATTCCAATGAAGATGAAGGAGGACTGTTTGGAGGCCAGGATCTTAAGTCAGGTAAAAGTTCCAGAAACC
TGAAATACAAAGATTTCTTTGATCCAGTTGAAAGTGATGAAGACGTAGCAAGTGTCCACGATGATGGGAATGAACTGGCT
TCAAATGAAGAGGAAGAGATTGCTGAAGGAGAAGAAAGCATTTCTGAGACGGATGAAGATGATGACCTTGAAGAAAGTGG
AGACAGTAAACAACGTAAAGAAACCTTGAAAAGAGTGACCTTTGCTCTGCCCAATGATGAGGACACTGAAGATACAAATG
TCTTAAATGTACAGAAAGACTCTGATGAAGTAAAATCCTCTTTTGAAAAAAGACAAGAAAAGATGAATGAAAAAATTGCA
TCTTTGGAAAAAGAGTTGTTGGAGAAGAAACCTTGGCAGCTTCAAGGAGAAGTGACAGCGCAGAAGCGGCCCGAGAACAG
CCTCCTGGAAGAGACCCTGCACTTCGACCACGCCGTGCGCATGGCACCTGTGATCACAGAGGAAACCACTCTCCAACTAG
AGGATATCATTAAGCAGAGGATAAAAGATCAGGCTTGGGATGATGTCGTACGCAAAGAAAAGCCTAAAGAGGATGCATTT
GAGTATAAAAAGCGTTTAACACTGGACCACGAAAAGAGTAAATTGAGCCTTGCTGAAATTTACGAACAGGAGTACATCAA
ACTCAACCAGCAAAAAACAGCAGAGGAAGAAAATCCAGAGCATGTAGAAATCCAGAAGATGATGGACTCCCTCTTCTTAA
AGTTGGATGTGCTCTCAAACTTCCACTTCATCCCCAAGCCACCTGTTCCAGAAATTAAAGTGGTATCAAATCTGCCCGCT
GTCACCATGGAGGAGGTTGCCCCTGTGAGTGTCAGTGACGCAGCCCTCCTGGCCCCAGAGGAGGTCAAGGAGAAAAATAA
AGCTGGAGATATAAAAACAGCTGCTGAGAAAACAGCTACAGAC

Alignment

ORF - retro_btau_1333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.78 %
• Parental protein coverage: 84.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARPAWRRRTLERCLREVGKATDSPECFLTIQDELASKFTSLTKVLYDFNKVLENDRKHGSPLKKLMINN
          MARPAWR.RTLERCLREVGKATDSPECFLTIQDELASK.TSLTKVLYDFNKVLENDRKHGSPL.KLMINN
Retrocopy MARPAWRWRTLERCLREVGKATDSPECFLTIQDELASKYTSLTKVLYDFNKVLENDRKHGSPLEKLMINN

Parental  FDDEQIWQQLELQNEPILQHFQSAVSETIEDEDISLLPESEEQECEEDVMELEAAGQEDLEQDLEEEEVE
          FDDEQIWQQLELQNEPILQHFQSAVSETIEDEDISLLPESEEQECEED.MELEAAGQEDLEQDLEEEEVE
Retrocopy FDDEQIWQQLELQNEPILQHFQSAVSETIEDEDISLLPESEEQECEEDMMELEAAGQEDLEQDLEEEEVE

Parental  EAEEVEVSDLSADDPEADERAKNSSKLDLRKSPDFSDEDSDLDFDISKLERQSKVQSRVPRKPTEKSI-V
          EAEEVEVSDLS.DDPEADERAKNSSKLDLRKSPDF....SD.D.D..........QS.V......K...V
Retrocopy EAEEVEVSDLSGDDPEADERAKNSSKLDLRKSPDF----SDEDSDLDFDISKLERQSKV*SRVPRKPT>V

Parental  DDKFFKLSEMETFLENMEKEEEQRDDQEEDDIDFFEDVDSDEDEGGLFGGQDLKSGKSSRNLKYKDFFDP
          DDKFFKLSEMETFLENMEKEEEQRDDQEEDDIDFFEDVDS.EDEGGLFGGQDLKSGKSSRNLKYKDFFDP
Retrocopy DDKFFKLSEMETFLENMEKEEEQRDDQEEDDIDFFEDVDSNEDEGGLFGGQDLKSGKSSRNLKYKDFFDP

Parental  VESDEDVASVQDDGNELASNEEEEIAEGEESISETDEDDDLEESGDSKQHKETLKRVTFALPNDEDTEDT
          VESDEDVASV.DDGNELASNEEEEIAEGEESISETDEDDDLEESGDSKQ.KETLKRVTFALPNDEDTEDT
Retrocopy VESDEDVASVHDDGNELASNEEEEIAEGEESISETDEDDDLEESGDSKQRKETLKRVTFALPNDEDTEDT

Parental  NILNVQKDSDEVKSSFEKRQEKMNEKIASLEKELLEKKPWQLQGEVTAQKRPENSLLEETLHFDHAVRMA
          N.LNVQKDSDEVKSSFEKRQEKMNEKIASLEKELLEKKPWQLQGEVTAQKRPENSLLEETLHFDHAVRMA
Retrocopy NVLNVQKDSDEVKSSFEKRQEKMNEKIASLEKELLEKKPWQLQGEVTAQKRPENSLLEETLHFDHAVRMA

Parental  PVITEETTLQLEDIIKQRIKDQAWDDVVRKEKPKEDAFEYKKRLTLDHEKSKLSLAEIYEQEYIKLNQQK
          PVITEETTLQLEDIIKQRIKDQAWDDVVRKEKPKEDAFEYKKRLTLDHEKSKLSLAEIYEQEYIKLNQQK
Retrocopy PVITEETTLQLEDIIKQRIKDQAWDDVVRKEKPKEDAFEYKKRLTLDHEKSKLSLAEIYEQEYIKLNQQK

Parental  TAEEENPEHVEIQKMMDSLFLKLDALSNFHFIPKPPVPEIKVVSNLPAVTMEEVAPVSVSDAALLAPEEV
          TAEEENPEHVEIQKMMDSLFLKLD.LSNFHFIPKPPVPEIKVVSNLPAVTMEEVAPVSVSDAALLAPEEV
Retrocopy TAEEENPEHVEIQKMMDSLFLKLDVLSNFHFIPKPPVPEIKVVSNLPAVTMEEVAPVSVSDAALLAPEEV

Parental  KEKNKAGDIKTAAEKTATD
          KEKNKAGDIKTAAEKTATD
Retrocopy KEKNKAGDIKTAAEKTATD

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	0.36 RPM	17.95 RPM
ERP005899_muscle	0.05 RPM	11.51 RPM
SRP017611_brain	0.00 RPM	9.96 RPM
SRP017611_kidney	0.06 RPM	16.66 RPM
SRP017611_liver	0.00 RPM	13.21 RPM
SRP030211_testis	0.18 RPM	36.18 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1333 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1333 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1333 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009854	1 retrocopy	retro_btau_1333 ,
Echinops telfairi	ENSETEG00000016641	1 retrocopy	retro_etel_1387,
Otolemur garnettii	ENSOGAG00000003177	1 retrocopy	retro_ogar_313,