RetrogeneDB ID: retro_ptro_681

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:33383345..33383952(+)
• Located in intron of: ENSPTRG00000005071

Retrocopy information

• Ensembl ID: ENSPTRG00000040311
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB13
• Ensembl ID: ENSPTRG00000001370
• Aliases: None
• Description: RAB13, member RAS oncogene family [Source:HGNC Symbol;Acc:9762]

Sequence

>retro_ptro_681
ATGGCCAAAGCCTACGACCACCTCTTCAAGTTGCTGCTGATCGGGGACTCGGGGGTGGGCAAGACTTGTCTGATCATTCG
CTTTGCAGAGGACAACTTCAACAACACTTACATCTCCACCATCGGAATTGATTTCAAGATCCGCACTGTGGATATAGAGG
GGAAGAAGATCAAACTACAAGTCTGGGACACGGCTGGCCAAGAGCGGTTCAAGACAATAACTACTGCCTACTACCGTGGA
GCCATGGGCATTATCCTAGCATACGACATCACGGATGAGAAATCTTTCGAGAATATTCAGAACTGGATGAAAAGCATCAT
GGAGAATGCCTCAGCTGGGGTGGAGCACCTCTTGCTAGGGAACAAATGTGACATGGAGGTCAAGAGGAAGGTGCAGAAGG
AGCAGGCCGATAAGTTGGCTCGAGAGCATGGAATCCGATTTTTCGAAACTAGTGCTAAATCCAGTATGAATGCGCGATGA
GGCTTTTAGTTCCCTGGCCCGGGACATCTTGCTCAAGTCAGGAGGCCGGAGATCAGGAAACGGCAACAAGCCTCCCAGTA
CTGACCTGAAAACTTGTGACATAAAGAACACCAACAAGTGCTCCCTG

Alignment

ORF - retro_ptro_681 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.55 %
• Parental protein coverage: 99.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAKAYDHLFKLLLIGDSGVGKTCLIIRFAEDNFNNTYISTIGIDFKIRTVDIEGKKIKLQVWDTAGQERF
          MAKAYDHLFKLLLIGDSGVGKTCLIIRFAEDNFNNTYISTIGIDFKIRTVDIEGKKIKLQVWDTAGQERF
Retrocopy MAKAYDHLFKLLLIGDSGVGKTCLIIRFAEDNFNNTYISTIGIDFKIRTVDIEGKKIKLQVWDTAGQERF

Parental  KTITTAYYRGAMGIILVYDITDEKSFENIQNWMKSIKENASAGVERLLLGNKCDMEAKRKVQKEQADKLA
          KTITTAYYRGAMGIIL.YDITDEKSFENIQNWMKSI.ENASAGVE.LLLGNKCDME.KRKVQKEQADKLA
Retrocopy KTITTAYYRGAMGIILAYDITDEKSFENIQNWMKSIMENASAGVEHLLLGNKCDMEVKRKVQKEQADKLA

Parental  REHGIRFFETSAKSSMNV-DEAFSSLARDILLKSGGRRSGNGNKPPSTDLKTCDKKNTNKCSL
          REHGIRFFETSAKSSMN..DEAFSSLARDILLKSGGRRSGNGNKPPSTDLKTCD.KNTNKCSL
Retrocopy REHGIRFFETSAKSSMNA>DEAFSSLARDILLKSGGRRSGNGNKPPSTDLKTCDIKNTNKCSL

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
SRP007412_brain_prefrontal_cortex	0.32 RPM	9.62 RPM
SRP007412_cerebellum	0.32 RPM	10.04 RPM
SRP007412_heart	0.17 RPM	26.23 RPM
SRP007412_kidney	0.76 RPM	73.28 RPM
SRP007412_liver	0.49 RPM	40.98 RPM
SRP007412_testis	0.32 RPM	32.46 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_681 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_681 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_681 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1122

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 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 ,
Pan troglodytes	ENSPTRG00000003915	1 retrocopy	retro_ptro_2892,
Pan troglodytes	ENSPTRG00000011989	1 retrocopy	retro_ptro_1727,