RetrogeneDB ID: retro_mmul_1637

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:142943917..142944220(+)
• Located in intron of: ENSMMUG00000030227

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF181
• Ensembl ID: ENSMMUG00000017824
• Aliases: None
• Description: E3 ubiquitin-protein ligase RNF181 [Source:RefSeq peptide;Acc:NP_001252843]

Sequence

>retro_mmul_1637
ATGGCATCCTATATCGATGAACACGACTGTGAGCCATTGGACCCTCGAGCAGGAGACTCAAACCAACATGGTGCTGGAGC
TCGCAAGGTCAATTTTCAATAGGATGGACTTTGAAGACTTGGGGTTGGTAGTAGATTGGGATCACCACCTGCCTCCACCA
GCTACCAATACTGTGGTTGAGAACCTCCCTATGGCAGTTATCAGAGGCTCTCAGTCTGAGCTCAAGTGCCCCATGTGTCT
TTTGGAATTTGAGGAGGAGGAGACTGCCATTGAGAGGCTTCCCATCACCTCTTCCATTGCAGC

Alignment

ORF - retro_mmul_1637 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.52 %
• Parental protein coverage: 66.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASYFDEHDCEPSDP-EQETRTNMLLELARSLFNRMDFEDLGLVVDWDHHLPPPAAKNVVENLPRTVIRG
          MASY.DEHDCEP.DP.EQET.TNM.LELARS.FNRMDFEDLGLVVDWDHHLPPPA...VVENLP..VIRG
Retrocopy MASYIDEHDCEPLDP>EQETQTNMVLELARSIFNRMDFEDLGLVVDWDHHLPPPATNTVVENLPMAVIRG

Parental  SQAELKCPVCLLEFEEEETAIEM-PCHHLFHSS
          SQ.ELKCP.CLLEFEEEETAIE....HHLFH.S
Retrocopy SQSELKCPMCLLEFEEEETAIER<ASHHLFHCS

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	9.86 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	14.76 RPM
SRP007412_cerebellum	0.00 RPM	7.43 RPM
SRP007412_heart	0.00 RPM	20.79 RPM
SRP007412_kidney	0.00 RPM	26.99 RPM
SRP007412_liver	0.00 RPM	24.54 RPM
SRP007412_testis	0.00 RPM	44.59 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1637 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1637 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1637 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3771
Pan troglodytes	retro_ptro_2557
Gorilla gorilla	retro_ggor_2537
Pongo abelii	retro_pabe_3083

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019647	3 retrocopies	retro_cjac_2423, retro_cjac_355, retro_cjac_3849,
Homo sapiens	ENSG00000168894	3 retrocopies	retro_hsap_1005, retro_hsap_3771, retro_hsap_938,
Macaca mulatta	ENSMMUG00000017824	3 retrocopies	retro_mmul_1128, retro_mmul_1637 , retro_mmul_808,
Pongo abelii	ENSPPYG00000012225	2 retrocopies	retro_pabe_3083, retro_pabe_807,
Pan troglodytes	ENSPTRG00000012138	2 retrocopies	retro_ptro_2557, retro_ptro_650,