RetrogeneDB ID: retro_mmul_179

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 19:21638893..21639163(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000014356
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: C4ORF52
• Ensembl ID: ENSMMUG00000006680
• Aliases: None
• Description: None

Sequence

>retro_mmul_179
GTGGGTAGCCAGGTTTCCGAGAGTGCAGGGAGGTCGGCGGGTCAGGGCAGCCTGGGGCCCAACGCCATGTCCCGAAACCT
GCGCACCGCGCTCATTTTCGGCAGCTTCATCTCCCTGATCGGCGCGGCCTTCTATCCCATCTACTTCCGACCCCTAATGA
GACTGGAAGACTACAGGAGGGAGCAAGCCATAAATCGGGCTGGAATTGTTCAAGAGGATGTGCAGCCACCAGGGTTAAAA
GTGTGGTCTGATCCATTTGGCAGGAAATGA

Alignment

ORF - retro_mmul_179 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.38 %
• Parental protein coverage: 83.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VGSQVSESAGRSAGQGSPGRNAMSRNLRTALIFGGFVSLIGAAFYPIYFRPLMRLEDYKREQAINRAGIV
          VGSQVSESAGRSAGQGS.G.NAMSRNLRTALIFG.F.SLIGAAFYPIYFRPLMRLEDY.REQAINRAGIV
Retrocopy VGSQVSESAGRSAGQGSLGPNAMSRNLRTALIFGSFISLIGAAFYPIYFRPLMRLEDYRREQAINRAGIV

Parental  QEDVQPPGLKVWSDPFGRK
          QEDVQPPGLKVWSDPFGRK
Retrocopy QEDVQPPGLKVWSDPFGRK

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	5.71 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.09 RPM
SRP007412_cerebellum	0.00 RPM	7.17 RPM
SRP007412_heart	0.00 RPM	12.01 RPM
SRP007412_kidney	0.00 RPM	20.07 RPM
SRP007412_liver	0.00 RPM	6.81 RPM
SRP007412_testis	0.45 RPM	5.62 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_179 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_179 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_179 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003897	1 retrocopy	retro_btau_95,
Dasypus novemcinctus	ENSDNOG00000004966	2 retrocopies	retro_dnov_1474, retro_dnov_1529,
Macropus eugenii	ENSMEUG00000002680	1 retrocopy	retro_meug_147,
Microcebus murinus	ENSMICG00000017222	1 retrocopy	retro_mmur_868,
Macaca mulatta	ENSMMUG00000006680	1 retrocopy	retro_mmul_179 ,
Nomascus leucogenys	ENSNLEG00000016894	1 retrocopy	retro_nleu_216,
Ictidomys tridecemlineatus	ENSSTOG00000004810	1 retrocopy	retro_itri_699,
Tupaia belangeri	ENSTBEG00000015052	2 retrocopies	retro_tbel_1277, retro_tbel_4083,