RetrogeneDB ID: retro_btau_109

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:81396270..81396510(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000030274
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CMC2
• Ensembl ID: ENSBTAG00000017009
• Aliases: CMC2, C18H16orf61
• Description: COX assembly mitochondrial protein 2 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q2NKR3]

Sequence

>retro_btau_109
ATGCATCCTGACTTATCTCCACACTTGCACACTGAAGAATGCAACGTCTTGATTAACTTGCTTAAGGAATGTCACAAAAA
TCACAGCATTCTGAAATTTTTTGGTCATTGCAATGATCTTGATCGGGAGATGAGAAAATGCTTGAAGAATGAGTACATGG
AAAAGAGGAACAAGAGCAGGGAGCTTGGCAACGCAATGCGAAAGAGACTTTTTAATCCTCCAGAGGAATCTGAAAACTAG

Alignment

ORF - retro_btau_109 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MHPDLSPHLHTEECNVLINLLKECHKNHSILKFFGHCNDLDREMRKCLKNEYMEKRNKSRELGNAMRKRL
          MHPDLSPHLHTEECNVLINLLKECHKNHSILKFFGHCNDLDREMRKCLKNEYMEKRNKSRELGNAMRKRL
Retrocopy MHPDLSPHLHTEECNVLINLLKECHKNHSILKFFGHCNDLDREMRKCLKNEYMEKRNKSRELGNAMRKRL

Parental  FNPPEESEN
          FNPPEESEN
Retrocopy FNPPEESEN

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	0.14 RPM	17.59 RPM
ERP005899_muscle	0.00 RPM	31.99 RPM
SRP017611_brain	0.32 RPM	10.78 RPM
SRP017611_kidney	0.12 RPM	14.46 RPM
SRP017611_liver	0.15 RPM	11.63 RPM
SRP030211_testis	0.15 RPM	24.61 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_109 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_109 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_109 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013929	2 retrocopies	retro_amel_397, retro_amel_681,
Bos taurus	ENSBTAG00000017009	1 retrocopy	retro_btau_109 ,
Echinops telfairi	ENSETEG00000010422	3 retrocopies	retro_etel_2190, retro_etel_357, retro_etel_816,
Felis catus	ENSFCAG00000004977	1 retrocopy	retro_fcat_193,
Loxodonta africana	ENSLAFG00000004378	2 retrocopies	retro_lafr_311, retro_lafr_896,
Microcebus murinus	ENSMICG00000011915	2 retrocopies	retro_mmur_1149, retro_mmur_701,
Monodelphis domestica	ENSMODG00000025763	1 retrocopy	retro_mdom_1670,
Sorex araneus	ENSSARG00000008906	2 retrocopies	retro_sara_712, retro_sara_84,
Sarcophilus harrisii	ENSSHAG00000001006	1 retrocopy	retro_shar_254,
Tupaia belangeri	ENSTBEG00000000038	3 retrocopies	retro_tbel_1840, retro_tbel_1979, retro_tbel_2249,