RetrogeneDB ID: retro_btau_1597

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:13426635..13427264(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CABP1
• Ensembl ID: ENSBTAG00000020049
• Aliases: None
• Description: Calcium-binding protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9N1R0]

Sequence

>retro_btau_1597
ATGGGCTACTGTGTCAAGTCTCCACTGGTCTGTCTCTCAAGGAAGATGTGCCAAGAGGAGACCAGCTACACAGTGATGCA
GATGAGTGAGGAGGGGCTGGCAGCCAGTGTGAGCTTCGCAGGCCCCTCTTGATGCTGGCTCAGAACTGCGCAGTCATGCA
CAACCTGCTGGGCCCAGCCTTCATCTTCCTGCATAAGGGCTTTGCAGAGAACAGGCAGCCTGACAGATCTCTGTGGCCAG
AGGAGATTGAAGAGCTCAGGGAGACCATCAGAAAATTTGACAAGGACGAAGATGGCTACATCAACTGCCGGGACCTGGGT
AACTGCATGCGCACCATGGGTTACATGCCCACAGAGATGGAGCTCATCGAGCTGTCCCAGCAGATCAATATGAACCGGGG
TGACCACTTGGATTTTGATGACTTTGTGGAACTAATGGGACCTAAACTCCTGGCGGAGACAGTAGATATAATTGGAGTAA
AGGAACTGTGAGATGCCTTCGGAGAGTTTGACACCAGTGGTGATGGGGAGATAAGCACCAGTGAGTTACCAGAGGCCATG
AGGAAACTCCTGGGCCATCAGGTGGGACACCGAGACATAGAGCAAATTATCCAAGTTGTGGACCTCAAT

Alignment

ORF - retro_btau_1597 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.78 %
• Parental protein coverage: 92.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGNCVKSPLRNLSRKMRQEETSYTVVQTSEEGLAASGELPGP-LLMLAQNCAVMHNLLGPACIFLRKGFA
          MG.CVKSPL..LSRKM.QEETSYTV.Q.SEEGLAAS....GP.LLMLAQNCAVMHNLLGPA.IFL.KGFA
Retrocopy MGYCVKSPLVCLSRKMCQEETSYTVMQMSEEGLAASVSFAGP<LLMLAQNCAVMHNLLGPAFIFLHKGFA

Parental  ENRQPDRSLRPEEIEELREAFREFDKDKDGYINCRDLGNCMRTMGYMPTEMELIELSQQINMNLGGHVDF
          ENRQPDRSL.PEEIEELRE..R.FDKD.DGYINCRDLGNCMRTMGYMPTEMELIELSQQINMN.G.H.DF
Retrocopy ENRQPDRSLWPEEIEELRETIRKFDKDEDGYINCRDLGNCMRTMGYMPTEMELIELSQQINMNRGDHLDF

Parental  DDFVELMGPKLLAETADMIGVKELRDAFREFDTNGDGEISTSELREAMRKLLGHQVGHRDIEEIIRDVDL
          DDFVELMGPKLLAET.D.IGVKEL.DAF.EFDT.GDGEISTSEL.EAMRKLLGHQVGHRDIE.II..VDL
Retrocopy DDFVELMGPKLLAETVDIIGVKEL*DAFGEFDTSGDGEISTSELPEAMRKLLGHQVGHRDIEQIIQVVDL

Parental  N
          N
Retrocopy N

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	0.00 RPM
ERP005899_muscle	0.00 RPM	0.05 RPM
SRP017611_brain	0.00 RPM	41.34 RPM
SRP017611_kidney	0.00 RPM	0.30 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP030211_testis	0.00 RPM	11.14 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1597 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1597 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1597 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014583	2 retrocopies	retro_btau_113, retro_btau_135,
Bos taurus	ENSBTAG00000020049	1 retrocopy	retro_btau_1597 ,