RetrogeneDB ID: retro_mmul_2392

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:35079105..35079276(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000021240
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.18539
• Ensembl ID: ENSMMUG00000031677
• Aliases: None
• Description: None

Sequence

>retro_mmul_2392
GACTGGCTGAGGGGCAAGGTGGAAGTCAATCAAGAGACTATCCAGCGGCTCCTTGAGGAGAATGAGCAACTGATCCTCTG
TATTGTGGAGTATCAGTACAAGGGCCGGGCAAACGAGTGCGTCCAGTGCCAGCATGTGTTACATAGAAATCTCATTTATT
TGGCTACCATC

Alignment

ORF - retro_mmul_2392 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.72 %
• Parental protein coverage: 74.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DWLMGKAEVNQETIQRLLEENDQLIRCIVEYQNKGRGNECVQYQHVLHRNLIYLATI
          DWL.GK.EVNQETIQRLLEEN.QLI.CIVEYQ.KGR.NECVQ.QHVLHRNLIYLATI
Retrocopy DWLRGKVEVNQETIQRLLEENEQLILCIVEYQYKGRANECVQCQHVLHRNLIYLATI

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	14.68 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	12.77 RPM
SRP007412_cerebellum	0.00 RPM	12.53 RPM
SRP007412_heart	0.00 RPM	9.72 RPM
SRP007412_kidney	0.00 RPM	8.10 RPM
SRP007412_liver	0.00 RPM	7.68 RPM
SRP007412_testis	0.08 RPM	8.90 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2392 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2392 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2392 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_557
Pongo abelii	retro_pabe_513

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000989	1 retrocopy	retro_acar_189,
Dipodomys ordii	ENSDORG00000015005	4 retrocopies	retro_dord_286, retro_dord_39, retro_dord_643, retro_dord_658,
Homo sapiens	ENSG00000008324	1 retrocopy	retro_hsap_557,
Loxodonta africana	ENSLAFG00000021542	2 retrocopies	retro_lafr_754, retro_lafr_92,
Myotis lucifugus	ENSMLUG00000013024	1 retrocopy	retro_mluc_21,
Macaca mulatta	ENSMMUG00000031677	1 retrocopy	retro_mmul_2392 ,
Nomascus leucogenys	ENSNLEG00000005848	1 retrocopy	retro_nleu_2639,
Ochotona princeps	ENSOPRG00000015198	4 retrocopies	retro_opri_401, retro_opri_516, retro_opri_542, retro_opri_593,
Pongo abelii	ENSPPYG00000013979	2 retrocopies	retro_pabe_513, retro_pabe_651,