RetrogeneDB ID: retro_btau_30

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 17:15274688..15274943(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000045665
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CCDC167
• Ensembl ID: ENSBTAG00000012069
• Aliases: CCDC167, C23H6orf129, C6orf129
• Description: Coiled-coil domain-containing protein 167 [Source:UniProtKB/Swiss-Prot;Acc:A1A4P9]

Sequence

>retro_btau_30
ATGATCGATGGGCTGGAGAAGAAGCTGTCACAATGTCGGAGAGACCTGGAAGTCGTGAACTCCAGGCTCTGTGGGGTGGA
GCTGAGCTCAGAGGCCAGGAGGTCTCTGGAGAAGGAGAAAAGCAGCCTGATGAACAAAGCCTCCAACTATGAGAAGGAGC
TGAAGTTGCTTCGGCAGGAGAACCGCAAGAACATGCTGCTGTCTGTGGCCATCTTCCTCCTGCTGACTGTCATCTATGCC
TACTGGGCCCTGTGA

Alignment

ORF - retro_btau_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 85.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IDGLEKKLSQCRRDLEVVNSRLCGVELSSEARRSLEKEKSSLMNKASNYEKELKLLRQENRKNMLLSVAI
          IDGLEKKLSQCRRDLEVVNSRLCGVELSSEARRSLEKEKSSLMNKASNYEKELKLLRQENRKNMLLSVAI
Retrocopy IDGLEKKLSQCRRDLEVVNSRLCGVELSSEARRSLEKEKSSLMNKASNYEKELKLLRQENRKNMLLSVAI

Parental  FLLLTVIYAYWAL
          FLLLTVIYAYWAL
Retrocopy FLLLTVIYAYWAL

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	12.54 RPM
ERP005899_muscle	0.11 RPM	18.42 RPM
SRP017611_brain	0.00 RPM	5.76 RPM
SRP017611_kidney	0.00 RPM	7.59 RPM
SRP017611_liver	0.15 RPM	27.11 RPM
SRP030211_testis	0.13 RPM	41.22 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_30 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_30 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_30 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012069	2 retrocopies	retro_btau_30 , retro_btau_517,
Canis familiaris	ENSCAFG00000030835	1 retrocopy	retro_cfam_1854,
Callithrix jacchus	ENSCJAG00000005622	2 retrocopies	retro_cjac_3293, retro_cjac_960,
Felis catus	ENSFCAG00000006745	1 retrocopy	retro_fcat_1558,
Mus musculus	ENSMUSG00000024018	1 retrocopy	retro_mmus_3487,
Otolemur garnettii	ENSOGAG00000000921	1 retrocopy	retro_ogar_880,
Pongo abelii	ENSPPYG00000016563	1 retrocopy	retro_pabe_2092,