RetrogeneDB ID: retro_btau_62

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:77154430..77154946(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000030890
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TTC9C
• Ensembl ID: ENSBTAG00000000773
• Aliases: None
• Description: Tetratricopeptide repeat protein 9C [Source:UniProtKB/Swiss-Prot;Acc:A4IFF3]

Sequence

>retro_btau_62
ATGGAGAAACGCCTGCAGGAGGCTCAGCTGTACAAGGAGAAAGGGAACCAGTGTTACCGGGAAGGGAAGTACCGGGATGC
TGTAAGTGGGTACCATCGAGCTCTGCTGCAGCTGCGGGGTCTGGATCCAAGTCTGCCCTCCCCGATACCTAATCTGGGAC
CTCAGGGCCTGGCCCTCACACCTGAACAAGAAAACCTACTTCACACCACCCAGACAGATTGCTACAACAACCTGGCTGCC
TGTCTCCTTCAGATGGAACCAGTAAACTATGAACGGGTGAAAGAGTACAGCCAGAAAGACGTGGAGCGGCAGCCTGATAA
TGCCAAGGCCTTGTATCGGGCTGGAGTGGCCTTTTTCCACCTGCAGGACTATGACCAGGCCCGGCACTACCTCATGGCTG
CTGTCAATAGGAAGCCAAAAGACGCCAATGTCCGGAGGTACCTTCAGCGGACACAGTTGGAACTCAGCAGCTACCATCGG
AAAGAGAAGCAGCTCTACCTGGGCATGTTTGGTTAA

Alignment

ORF - retro_btau_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEKRLQEAQLYKEKGNQCYREGKYRDAVSGYHRALLQLRGLDPSLPSPIPNLGPQGPALTPEQENLLHTT
          MEKRLQEAQLYKEKGNQCYREGKYRDAVSGYHRALLQLRGLDPSLPSPIPNLGPQG.ALTPEQENLLHTT
Retrocopy MEKRLQEAQLYKEKGNQCYREGKYRDAVSGYHRALLQLRGLDPSLPSPIPNLGPQGLALTPEQENLLHTT

Parental  QTDCYNNLAACLLQMEPVNYERVKEYSQKVLERQPDNAKALYRAGVAFFHLQDYDQARHYLMAAVNRKPK
          QTDCYNNLAACLLQMEPVNYERVKEYSQK..ERQPDNAKALYRAGVAFFHLQDYDQARHYLMAAVNRKPK
Retrocopy QTDCYNNLAACLLQMEPVNYERVKEYSQKDVERQPDNAKALYRAGVAFFHLQDYDQARHYLMAAVNRKPK

Parental  DANVRRYLQRTQLELSSYHRKEKQLYLGMFG
          DANVRRYLQRTQLELSSYHRKEKQLYLGMFG
Retrocopy DANVRRYLQRTQLELSSYHRKEKQLYLGMFG

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	0.07 RPM	9.52 RPM
ERP005899_muscle	0.16 RPM	18.21 RPM
SRP017611_brain	0.14 RPM	7.40 RPM
SRP017611_kidney	0.24 RPM	11.08 RPM
SRP017611_liver	0.00 RPM	4.15 RPM
SRP030211_testis	0.36 RPM	12.19 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_62 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_62 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_62 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000773	2 retrocopies	retro_btau_62 , retro_btau_78,