RetrogeneDB ID: retro_mmul_324

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:73668574..73668943(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000031740
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.4654
• Ensembl ID: ENSMMUG00000017586
• Aliases: None
• Description: ras-related protein Rab-13 [Source:RefSeq peptide;Acc:NP_001248220]

Sequence

>retro_mmul_324
ATGGGTATTATCCTAGTATACGACATCATGGATGAGAAATCTTTCGAGAATATTCAGAACTGGATGAAAAGCATCAAGGA
GAATGGCTTGGCTGGGGTGGAACACCTCTTGCTAGGGAACAAATGTGACGTGGAGGCCAAGAGGAAGGTGCAAAAGGAGC
AGGCCGATAAGTTGGCTCCAGAGCAAGGAATCCGATTTTTCGAAACTAGTGCTAAATCCAGTATGAATGTGGATGAGGCT
TTTAGCTCCCTGGCCCAGGACATCTTGCTCAAGTCAGGAGACCGGAGATCAGGAAACGGCAACAAGCCTCCCAGTACTGA
CCTGAAAACTTGCGACAAGAAGAACACCAGCAAGTGCTCCCTGGGCTGA

Alignment

ORF - retro_mmul_324 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.8 %
• Parental protein coverage: 60.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGIILVYDITDEKSFENIQNWMKSIKENASAGVERLLLGNKCDMEAKRKVQKEQADKLAREHGIRFFETS
          MGIILVYDI.DEKSFENIQNWMKSIKEN..AGVE.LLLGNKCD.EAKRKVQKEQADKLA.E.GIRFFETS
Retrocopy MGIILVYDIMDEKSFENIQNWMKSIKENGLAGVEHLLLGNKCDVEAKRKVQKEQADKLAPEQGIRFFETS

Parental  AKSSMNVDEAFSSLARDILLKSGGRRSGNGNKPPSTDLKTCDKKNTNKCSLG
          AKSSMNVDEAFSSLA.DILLKSG.RRSGNGNKPPSTDLKTCDKKNT.KCSLG
Retrocopy AKSSMNVDEAFSSLAQDILLKSGDRRSGNGNKPPSTDLKTCDKKNTSKCSLG

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	0.00 RPM	10.20 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	10.47 RPM
SRP007412_cerebellum	0.00 RPM	13.69 RPM
SRP007412_heart	0.06 RPM	43.28 RPM
SRP007412_kidney	0.00 RPM	45.19 RPM
SRP007412_liver	0.00 RPM	25.85 RPM
SRP007412_testis	0.15 RPM	31.51 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_324 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_324 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_324 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 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 ,
Macaca mulatta	ENSMMUG00000021721	1 retrocopy	retro_mmul_951,
Otolemur garnettii	ENSOGAG00000016969	1 retrocopy	retro_ogar_2441,
Pan troglodytes	ENSPTRG00000001370	1 retrocopy	retro_ptro_681,