RetrogeneDB ID: retro_mmul_2112

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:130126206..130126539(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC24
• Ensembl ID: ENSMMUG00000006845
• Aliases: None
• Description: dnaJ homolog subfamily C member 24 [Source:RefSeq peptide;Acc:NP_001248674]

Sequence

>retro_mmul_2112
TATCATTCATATTAACAAAGTACAGATGTGCCAGCAGGAATAGTGGAGGACTGTAAACAGAAATTCATTGAAATTGATCA
GGCATGGAAAATTCTAGGGAATGAAGAGAAAAAAAAAGAGTATGACCCTCAGTGGCATGAAGATGATCTAAGATACATGG
AGCCAGTAGATGCTCAAGGATATCTTGAAAAACTGTCTTGGAAAAATGACGATGACTCTTTTTCCCCAAGTTGCCAATGT
GGTAGAAAACACAGTGTTTCCAAGGATGAAGCAGAAGAAGTTAATCTATTTTCTTGTGATATATGTTCGCTATTTATAGA
ACTTCTTCATTAT

Alignment

ORF - retro_mmul_2112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.07 %
• Parental protein coverage: 99.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YHPDKQSTDVSAGTVEECVQKFIEIDQAWKILGNEETKREYDLQRCEDDLRNIGPVDAQVYLEEMSWNED
          YH...QSTDV.AG.VE.C.QKFIEIDQAWKILGNEE...EYD.Q..EDDLR...PVDAQ.YLE..SW..D
Retrocopy YHSY*QSTDVPAGIVEDCKQKFIEIDQAWKILGNEEXXXEYDPQWHEDDLRYMEPVDAQGYLEKLSWKND

Parental  DHSFYLSCRCGGKYSVSKDEAEEVSLISCDTCSLIIELLHY
          D.SF..SC.CG.K.SVSKDEAEEV.L.SCD.CSL.IELLHY
Retrocopy DDSFSPSCQCGRKHSVSKDEAEEVNLFSCDICSLFIELLHY

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	3.03 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	1.19 RPM
SRP007412_cerebellum	0.00 RPM	3.36 RPM
SRP007412_heart	0.00 RPM	1.59 RPM
SRP007412_kidney	0.00 RPM	2.00 RPM
SRP007412_liver	0.00 RPM	0.91 RPM
SRP007412_testis	0.00 RPM	4.67 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2112 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2112 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2301
Pongo abelii	retro_pabe_2783

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013512	1 retrocopy	retro_dnov_2247,
Dipodomys ordii	ENSDORG00000000248	3 retrocopies	retro_dord_221, retro_dord_395, retro_dord_77,
Echinops telfairi	ENSETEG00000003054	1 retrocopy	retro_etel_161,
Microcebus murinus	ENSMICG00000007553	3 retrocopies	retro_mmur_1052, retro_mmur_1150, retro_mmur_973,
Macaca mulatta	ENSMMUG00000006845	1 retrocopy	retro_mmul_2112 ,
Nomascus leucogenys	ENSNLEG00000017878	1 retrocopy	retro_nleu_3029,
Otolemur garnettii	ENSOGAG00000007848	1 retrocopy	retro_ogar_1542,
Ochotona princeps	ENSOPRG00000001638	1 retrocopy	retro_opri_881,
Pongo abelii	ENSPPYG00000003390	2 retrocopies	retro_pabe_2783, retro_pabe_2788,
Pan troglodytes	ENSPTRG00000003471	1 retrocopy	retro_ptro_2301,
Tarsius syrichta	ENSTSYG00000009243	1 retrocopy	retro_tsyr_623,