RetrogeneDB ID: retro_btau_517

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 13:62638088..62638372(+)
• Located in intron of: None

Retrocopy information

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

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_517
ACTAAAATGAAGCAAGACAATTTGGGCATCACTCTAGAGATTCATGGGCTAGAAAGAAGCTGCCACAATGTCAGAGAGAC
CTGGAGGCTGTGAACTCCAGGCTCTGTGGGGCGGAGCTGAGCTCAGAGCCCAGGAGGTCTCTGGAGAAGGAGAAAAGCAG
CCTGATGAACAAAGCCTCCAACTATGAGAAGGAGCTGAAATTGGTTCGGCAGGAGAACCACAGGGACATGCTGCTGTCTG
TGGCCACCTTCCTCCTCCTGACCCTCGTCTACGCCTCCTGGGCC

Alignment

ORF - retro_btau_517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.17 %
• Parental protein coverage: 97.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TKKKRENLGVALEIDGLE-KKLSQCRRDLEVVNSRLCGVELSSEARRSLEKEKSSLMNKASNYEKELKLL
          TK.K..NLG..LEI.GLE.KKL.QC.RDLE.VNSRLCG.ELSSE.RRSLEKEKSSLMNKASNYEKELKL.
Retrocopy TKMKQDNLGITLEIHGLE<KKLPQCQRDLEAVNSRLCGAELSSEPRRSLEKEKSSLMNKASNYEKELKLV

Parental  RQENRKNMLLSVAIFLLLTVIYAYWA
          RQEN...MLLSVA.FLLLT..YA.WA
Retrocopy RQENHRDMLLSVATFLLLTLVYASWA

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	0.00 RPM	18.42 RPM
SRP017611_brain	0.00 RPM	5.76 RPM
SRP017611_kidney	0.00 RPM	7.59 RPM
SRP017611_liver	0.00 RPM	27.11 RPM
SRP030211_testis	0.01 RPM	41.22 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_517 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_517 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_517 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,