RetrogeneDB ID: retro_mmul_114

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:49380248..49380710(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000029619
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.1947
• Ensembl ID: ENSMMUG00000012053
• Aliases: None
• Description: None

Sequence

>retro_mmul_114
AAGTTAATAAAGGTATCCACGGAGAACACTGAAAACTCGGTGGATTCAAAATCCATTAAAAGTTTGGAACCAAAGATCAT
ACATGGAAGCAAATCAGTGGACTCTGGAATATCCCTGGACTACAGTTATAAAATGGATTATCCTGAGATGGGTTTATGTA
TAATAATTAATAATAAGAATTTTCATAAAAGCACTGGAATGGGATCTCGGTCTGGTACAGATGTTGATGCAGCAAACCTC
AGGGAAACATTCATAAACTTGAAATATGAAGTCAGGAATAAAAACGATCTTACATGTGAAGAAATTGTGGAATTGATGCG
CAATGTTTCTAGAGAAGATCACAGCAAAAGGCGCAGTTTTGTTTGTGTGCTTCTGAGCCATAGTGAAGAAGGAATAAGTT
TTGGAACAAATGGACCTGTTGACCTGAAAAAAATAACAAGCTTTTTCAGAGTGGATTGTTGT

Alignment

ORF - retro_mmul_114 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.2 %
• Parental protein coverage: 53.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENTENSVDSKSIKSLEPKIIHGSKSVDSGISLENSYKMDYPEMGLCIIINNKNFHKSTGMASRSGTDVDA
          ENTENSVDSKSIKSLEPKIIHGSKSVDSGISL..SYKMDYPEMGLCIIINNKNFHKSTGM.SRSGTDVDA
Retrocopy ENTENSVDSKSIKSLEPKIIHGSKSVDSGISLDYSYKMDYPEMGLCIIINNKNFHKSTGMGSRSGTDVDA

Parental  ANLRETFINLKYEVRNKNDLTREEIVELMRNVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPLDLKKITS
          ANLRETFINLKYEVRNKNDLT.EEIVELMRNVS.EDHSKR.SFVCVLLSH.EEGI.FGTNGP.DLKKITS
Retrocopy ANLRETFINLKYEVRNKNDLTCEEIVELMRNVSREDHSKRRSFVCVLLSHSEEGISFGTNGPVDLKKITS

Parental  FFRGDCC
          FFR.DCC
Retrocopy FFRVDCC

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	0.11 RPM	7.40 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	5.08 RPM
SRP007412_cerebellum	0.06 RPM	6.20 RPM
SRP007412_heart	0.00 RPM	2.94 RPM
SRP007412_kidney	0.00 RPM	3.05 RPM
SRP007412_liver	0.04 RPM	1.98 RPM
SRP007412_testis	0.08 RPM	1.47 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_114 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_114 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_114 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005740	2 retrocopies	retro_cjac_2678, retro_cjac_3011,
Cavia porcellus	ENSCPOG00000012511	2 retrocopies	retro_cpor_1203, retro_cpor_1450,
Dasypus novemcinctus	ENSDNOG00000013931	1 retrocopy	retro_dnov_1013,
Dipodomys ordii	ENSDORG00000002554	2 retrocopies	retro_dord_178, retro_dord_620,
Homo sapiens	ENSG00000164305	1 retrocopy	retro_hsap_406,
Gorilla gorilla	ENSGGOG00000025155	1 retrocopy	retro_ggor_402,
Microcebus murinus	ENSMICG00000004809	2 retrocopies	retro_mmur_1389, retro_mmur_691,
Macaca mulatta	ENSMMUG00000012053	1 retrocopy	retro_mmul_114 ,
Nomascus leucogenys	ENSNLEG00000010895	1 retrocopy	retro_nleu_1005,
Otolemur garnettii	ENSOGAG00000005985	2 retrocopies	retro_ogar_1756, retro_ogar_3263,
Pongo abelii	ENSPPYG00000015236	1 retrocopy	retro_pabe_312,
Pan troglodytes	ENSPTRG00000016640	1 retrocopy	retro_ptro_310,
Rattus norvegicus	ENSRNOG00000010475	1 retrocopy	retro_rnor_2747,
Sarcophilus harrisii	ENSSHAG00000009178	1 retrocopy	retro_shar_404,
Ictidomys tridecemlineatus	ENSSTOG00000003865	2 retrocopies	retro_itri_172, retro_itri_586,