RetrogeneDB ID: retro_mmul_497

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:62469421..62469667(-)
• Located in intron of: ENSMMUG00000002387

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1733
• Ensembl ID: ENSMMUG00000022692
• Aliases: ZCSL2, DPH3
• Description: DPH3, KTI11 homolog [Source:RefSeq peptide;Acc:NP_001247449]

Sequence

>retro_mmul_497
ATGGCAGTGTTTCATGACGAGGTAGAAATAGAGGACTTCCAACATGATGAGGACTCAGAGACATATTTCTATCCCTGCCC
ATGTGGAGATAACTTCTCCATTACCAAGGAAGATTTGGAGAATGGGGACGACGTGGCAATGTGTCCTAGCTGCTCTCTCA
TTATAAAAGGGATTTATGACAAAGATCCGTTTGTGTGTGCAGAAACAGTCCCAGCCCCTTTAGCCAACATAGAACTAGTT
AAGTGC

Alignment

ORF - retro_mmul_497 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.24 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVFHDEVEIEDFQYDEDSETYFYPCPCGDNFSITKEDLENGEDVATCPSCSLIIKVIYDKDQFVCGETV
          MAVFHDEVEIEDFQ.DEDSETYFYPCPCGDNFSITKEDLENG.DVA.CPSCSLIIK.IYDKD.FVC.ETV
Retrocopy MAVFHDEVEIEDFQHDEDSETYFYPCPCGDNFSITKEDLENGDDVAMCPSCSLIIKGIYDKDPFVCAETV

Parental  PAPSANKELVKC
          PAP.AN.ELVKC
Retrocopy PAPLANIELVKC

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	39.55 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	30.62 RPM
SRP007412_cerebellum	0.00 RPM	31.12 RPM
SRP007412_heart	0.06 RPM	31.09 RPM
SRP007412_kidney	0.00 RPM	30.52 RPM
SRP007412_liver	0.04 RPM	17.54 RPM
SRP007412_testis	0.00 RPM	32.98 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_497 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_497 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_497 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012030	1 retrocopy	retro_dnov_39,
Dipodomys ordii	ENSDORG00000011642	1 retrocopy	retro_dord_167,
Erinaceus europaeus	ENSEEUG00000009790	1 retrocopy	retro_eeur_502,
Echinops telfairi	ENSETEG00000016272	1 retrocopy	retro_etel_1879,
Homo sapiens	ENSG00000154813	1 retrocopy	retro_hsap_2438,
Gorilla gorilla	ENSGGOG00000022108	1 retrocopy	retro_ggor_174,
Loxodonta africana	ENSLAFG00000025650	3 retrocopies	retro_lafr_31, retro_lafr_545, retro_lafr_87,
Macaca mulatta	ENSMMUG00000022692	2 retrocopies	retro_mmul_2085, retro_mmul_497 ,
Monodelphis domestica	ENSMODG00000025472	3 retrocopies	retro_mdom_131, retro_mdom_1434, retro_mdom_609,
Mus musculus	ENSMUSG00000021905	1 retrocopy	retro_mmus_196,
Nomascus leucogenys	ENSNLEG00000001096	2 retrocopies	retro_nleu_2876, retro_nleu_2913,
Pongo abelii	ENSPPYG00000014083	1 retrocopy	retro_pabe_1795,
Pan troglodytes	ENSPTRG00000014671	1 retrocopy	retro_ptro_1409,
Tupaia belangeri	ENSTBEG00000011675	1 retrocopy	retro_tbel_58,
Tursiops truncatus	ENSTTRG00000007739	3 retrocopies	retro_ttru_1474, retro_ttru_31, retro_ttru_907,