RetrogeneDB ID: retro_mmul_1693

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:82479766..82480069(-)
• Located in intron of: ENSMMUG00000017382

Retrocopy information

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

Parental gene information

• Parental gene symbol: VMA21
• Ensembl ID: ENSMMUG00000009034
• Aliases: None
• Description: VMA21 vacuolar H+-ATPase homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:22082]

Sequence

>retro_mmul_1693
GTGGAGCGCCCGGATAAAGCGGCACTGAACGCACTGCAGCCTCCTAAGTTCAGAAAAGAAAGCTCATTAGCGTCTACACT
GAAGACACTCCTGTTCTTCACAGCTTTAATGATCACCGTTCCTATTGGGTTATATTTCACAACTAAATCTTACATATTTG
AAGGCACCCTTGGGATGTCCAATAGGGACAGATATTTTTATGCTGCTAGTGTTGCAGTGGTCGGCGGCCATGTGGTGCTG
GCCCTCTTTATGTATGTGGCCTGGAATGAAGACTCACGACAGTGGTGTGAAGGCAAACAGGAT

Alignment

ORF - retro_mmul_1693 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.11 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MERPDKAALNALQPPEFRNESSLASTLKTLLFFTALMITVPIGLYFTTKSYIFEGALGMSNRDSYFYAAI
          .ERPDKAALNALQPP.FR.ESSLASTLKTLLFFTALMITVPIGLYFTTKSYIFEG.LGMSNRD.YFYAA.
Retrocopy VERPDKAALNALQPPKFRKESSLASTLKTLLFFTALMITVPIGLYFTTKSYIFEGTLGMSNRDRYFYAAS

Parental  VAVVAVHVVLALFVYVAWNEGSRQWREGKQD
          VAVV..HVVLALF.YVAWNE.SRQW.EGKQD
Retrocopy VAVVGGHVVLALFMYVAWNEDSRQWCEGKQD

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	0.22 RPM	7.62 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.25 RPM
SRP007412_cerebellum	0.26 RPM	6.52 RPM
SRP007412_heart	0.06 RPM	4.06 RPM
SRP007412_kidney	0.12 RPM	6.57 RPM
SRP007412_liver	0.00 RPM	3.01 RPM
SRP007412_testis	0.00 RPM	1.62 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1693 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1693 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1693 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3724
Pongo abelii	retro_pabe_3133

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006296	1 retrocopy	retro_btau_1106,
Callithrix jacchus	ENSCJAG00000003916	1 retrocopy	retro_cjac_150,
Dasypus novemcinctus	ENSDNOG00000008426	1 retrocopy	retro_dnov_504,
Homo sapiens	ENSG00000160131	1 retrocopy	retro_hsap_3724,
Macaca mulatta	ENSMMUG00000009034	1 retrocopy	retro_mmul_1693 ,
Mus musculus	ENSMUSG00000073131	2 retrocopies	retro_mmus_116, retro_mmus_3675,
Nomascus leucogenys	ENSNLEG00000013711	1 retrocopy	retro_nleu_1971,
Oryctolagus cuniculus	ENSOCUG00000015201	1 retrocopy	retro_ocun_443,
Pongo abelii	ENSPPYG00000020820	1 retrocopy	retro_pabe_3133,
Rattus norvegicus	ENSRNOG00000049744	1 retrocopy	retro_rnor_2843,
Ictidomys tridecemlineatus	ENSSTOG00000011179	1 retrocopy	retro_itri_500,