RetrogeneDB ID: retro_btau_1360

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:95289094..95289662(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLF16
• Ensembl ID: ENSBTAG00000038055
• Aliases: None
• Description: None

Sequence

>retro_btau_1360
CAGCCAGCCCCGGCCTCCAGCGCAGCCGAGGTCTCGGGACCCATGCACTCCTCCGGCGCGCTCGAGGTCCCTGGCGCGCC
AGCCGTCCCGGGAGCGTCTGCCCACCCTGGCGCGGTGTCTGGCGTGGCCCCTGGGGCCGGCCCCGCCCCCGCCACGGGTC
CAGGCCCCCGTCGGAGGCCAGTAACACCTGCTGCCAAGCGCCATCGCTGCCCCTTCCCGGGCTGCAACAAAGCCTATTAC
AAGTCATCACATCTGAAGTCCCACCAGCGCACCCACACGGGTGAGCGCCCGTTCTCCTGCGACTGGCTCGACTGCGACAA
GAAGTTTACGCGCTCCGACGAGCTGGCCCGCCACTACAGGACGCACACGGGCGAGAAACGCTTCTCCTGCCCACTCTGCC
CCAAGCAGTTCTCTCGGAGCGACCACCTGACCAAGCACGCCCGCCGCCACCCATCCTACCATCCTGATATGATCGAGTAC
AGGGGGCGCCGTCGCACGCCCCGCGTCGACCCGCAACCCGCCAACCTGGTGGACAGCTCCGGCTCCGTCCCCGGGCAGGT
GCCCAGCT

Alignment

ORF - retro_btau_1360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.44 %
• Parental protein coverage: 94.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RPGPGGSVRGRGGPPPAARLSARWASPRGGGARAEQSAAPGGASPASSSSAASSPSSGRAPGAAPAAAKS
          .P.P..S.....GP............P...GA.A...A...G..P......A..P...R.P.....AAK.
Retrocopy QPAPASSAAEVSGPMHSSGALEVPGAPAVPGASAHPGAV-SGVAPGAGPAPATGPGPRRRP--VTPAAKR

Parental  HRCPFPGCAKAYYKSSHLKSHLRTHTGERPFACDWPGCDKKFARSDELARHHRTHTGEKRFPCPLCSKRF
          HRCPFPGC.KAYYKSSHLKSH.RTHTGERPF.CDW..CDKKF.RSDELARH.RTHTGEKRF.CPLC.K.F
Retrocopy HRCPFPGCNKAYYKSSHLKSHQRTHTGERPFSCDWLDCDKKFTRSDELARHYRTHTGEKRFSCPLCPKQF

Parental  TRSDHLTKHARRHPGFRPELLRRQGTRSTSPSDSLPCSLAGS-PAPSPVPSPA
          .RSDHLTKHARRHP...P......G.R.T...D..P..L..S.PAPSP...PA
Retrocopy SRSDHLTKHARRHPSYHPDMIEYRGRRRTPRVDPQPANLVDS>PAPSPGRCPA

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	0.07 RPM
ERP005899_muscle	0.00 RPM	3.38 RPM
SRP017611_brain	0.00 RPM	3.75 RPM
SRP017611_kidney	0.00 RPM	2.67 RPM
SRP017611_liver	0.08 RPM	2.04 RPM
SRP030211_testis	0.08 RPM	4.29 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1360 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1360 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1360 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013740	1 retrocopy	retro_btau_1617,
Bos taurus	ENSBTAG00000017488	1 retrocopy	retro_btau_271,
Bos taurus	ENSBTAG00000020355	1 retrocopy	retro_btau_521,
Bos taurus	ENSBTAG00000038055	1 retrocopy	retro_btau_1360 ,