RetrogeneDB ID: retro_btau_1291

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:86172514..86173067(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BIN3
• Ensembl ID: ENSBTAG00000005470
• Aliases: None
• Description: bridging integrator 3 [Source:RefSeq peptide;Acc:NP_001068767]

Sequence

>retro_btau_1291
GTGGAGAGAGACTTTGAAACAGTGTATGGAAAATTCCAGCAACTGGAAGAGCAGACCAGGAGGCTGCAAAAGGACATGAA
GAGAAGCCCCAGTGCTGACTTGGCTATCAAATTGGCTGTGGAGGTGTCCTTAGACTTACTCTCTAATCCCCTCTCCAGTA
AGACCAGGACTTTATGAATGTGATGGCCATCCTGGACATGGTCATGAAGTGGATGGATCCCTTTAGCCAGGGAAAGTTTA
ATCAGATCCAAAAGACCATGGTTGACCCCTGAAAAAGTTTGACAGTGTCTCCCAGAACCTCAACATGGTGGTGGGAAGCA
GCCTTCCTATAGAGTAGGACTATAGGTGACTTCAGGACAAGATGGAGAAGTATCAGCCAAAGGAAAAGACAAGATCAGTG
CTCCCCAAACTCCACCAGGCCCCAGAAGAGCTTCAGCTTGCATGGGATGACCTTGAAACCAAGATCAAACAGCTCCTGGA
TGAGCTACTGAGGTTCTAAAACAGCTGATTACACTCCTTCTAGCCCAGCTTTGAGTCCCTGATCCAAGAGCAG

Alignment

ORF - retro_btau_1291 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.77 %
• Parental protein coverage: 73.52 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VERDFEREYGKLQQLEEQTKRLQKDMKKSTDADLAMSKSAVKISLDLLSNPLCEQ-DQDFLNMVTALDTA
          VERDFE..YGK.QQLEEQT.RLQKDMK.S..ADLA..K.AV..SLDLLSNPL....DQDF.N....LD..
Retrocopy VERDFETVYGKFQQLEEQTRRLQKDMKRSPSADLAI-KLAVEVSLDLLSNPLSSK<DQDFMNVMAILDMV

Parental  MKRMDAFNQEKVNQIQKTVIEP-LKKFGSVFPSLNMAVKRREQALQDYRRLQAKVEKYEEKEKTGPVLAK
          MK.MD.F.Q.K.NQIQKT...P.LKKF.SV...LNM.V........DYR.LQ.K.EKY..KEKT..VL.K
Retrocopy MKWMDPFSQGKFNQIQKTMVDP<LKKFDSVSQNLNMVVGSSLPIE*DYR*LQDKMEKYQPKEKTRSVLPK

Parental  LHQAREELRPVRDDFEAKNKQLLDEMPRFYNSRLDYFQPSFESLIRAQ
          LHQA.EEL....DD.E.K.KQLLDE..RF.NS.L..F.PSFESLI..Q
Retrocopy LHQAPEELQLAWDDLETKIKQLLDELLRF*NS*LHSF*PSFESLIQEQ

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	6.92 RPM
ERP005899_muscle	0.00 RPM	27.45 RPM
SRP017611_brain	0.00 RPM	7.13 RPM
SRP017611_kidney	0.00 RPM	27.74 RPM
SRP017611_liver	0.00 RPM	23.48 RPM
SRP030211_testis	0.00 RPM	24.35 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1291 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1291 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1291 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005470	1 retrocopy	retro_btau_1291 ,
Macropus eugenii	ENSMEUG00000002173	1 retrocopy	retro_meug_545,
Myotis lucifugus	ENSMLUG00000005585	1 retrocopy	retro_mluc_1238,
Monodelphis domestica	ENSMODG00000009297	1 retrocopy	retro_mdom_346,
Pteropus vampyrus	ENSPVAG00000006191	1 retrocopy	retro_pvam_1028,