RetrogeneDB ID: retro_cfam_1756

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:22405721..22406267(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000014235
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB13
• Ensembl ID: ENSCAFG00000017389
• Aliases: None
• Description: RAB13, member RAS oncogene family [Source:HGNC Symbol;Acc:9762]

Sequence

>retro_cfam_1756
ATGGCCAAAGCCTACGACCACCTCTTCAAGTTGCTGCTCATTGGGGACTCGGGCATGCGCAAGACCTGTCTCATCATTTG
CTTTGCCGAGGACAGCTTCAACAACACCTACATCTCCACCATTGGAATTGACTTCAAGATCTGCACTGTGGATATAGGAA
GGAAGAAGATCAAGTTGCAGATCTGGGACACAGCTGGCCAGGAGGGATTCAAGACAATAACTACTGCATATTACCGTGGA
GCCATGGGCATTATCCTCGTATATGACATCACAGATGAGAAATCCTTTGAGAATATTCAGAACTGGATGAAAAGCATCAA
AGAGAATGCCTCAGCTGGGGTGGAGCGCCTGCTTCTGGGGAACAAGTGTGATATGGAGGCCAAGAGGAAGGTACAGAAGG
AGCAGGTCATCAAGCTGGCTCGAGAGCATGGAATCCGATTCTTTGAGACAAGTGCCAAATCCAGCACGAATGTGGATGAG
GCTTTCAGTTCCCTGGCCTGGGACATCCTGCTCAAGTCAGGAGGCCAGAGATCAGGAAACAGCCAC

Alignment

ORF - retro_cfam_1756 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.41 %
• Parental protein coverage: 89.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKAYDHLFKLLLIGDSGVGKTCLIIRFAEDSFNNTYISTIGIDFKIRTVDVEGKKIKLQVWDTAGQERF
          MAKAYDHLFKLLLIGDSG..KTCLII.FAEDSFNNTYISTIGIDFKI.TVD...KKIKLQ.WDTAGQE.F
Retrocopy MAKAYDHLFKLLLIGDSGMRKTCLIICFAEDSFNNTYISTIGIDFKICTVDIGRKKIKLQIWDTAGQEGF

Parental  KTITTAYYRGAMGIILVYDITDEKSFENIQNWMKSIKENASAGVERLLLGNKCDMEAKRKVQKEQAIKLA
          KTITTAYYRGAMGIILVYDITDEKSFENIQNWMKSIKENASAGVERLLLGNKCDMEAKRKVQKEQ.IKLA
Retrocopy KTITTAYYRGAMGIILVYDITDEKSFENIQNWMKSIKENASAGVERLLLGNKCDMEAKRKVQKEQVIKLA

Parental  REHGIRFFETSAKSSTNVDEAFSSLARDILLKSGGRRSGNSH
          REHGIRFFETSAKSSTNVDEAFSSLA.DILLKSGG.RSGNSH
Retrocopy REHGIRFFETSAKSSTNVDEAFSSLAWDILLKSGGQRSGNSH

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
SRP012049_cerebellum	0.08 RPM	9.07 RPM
SRP017611_brain	0.00 RPM	8.02 RPM
SRP017611_kidney	0.00 RPM	14.59 RPM
SRP017611_liver	0.00 RPM	6.02 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1756 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1756 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1756 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017389	1 retrocopy	retro_cfam_1756 ,
Homo sapiens	ENSG00000143545	1 retrocopy	retro_hsap_1122,
Loxodonta africana	ENSLAFG00000032079	1 retrocopy	retro_lafr_45,
Macaca mulatta	ENSMMUG00000017586	1 retrocopy	retro_mmul_324,
Otolemur garnettii	ENSOGAG00000016969	1 retrocopy	retro_ogar_2441,
Pan troglodytes	ENSPTRG00000001370	1 retrocopy	retro_ptro_681,