RetrogeneDB ID: retro_mmul_2080

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:53207305..53207789(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.811
• Ensembl ID: ENSMMUG00000001079
• Aliases: AK4, AK3, AK3L1
• Description: None

Sequence

>retro_mmul_2080
CCCACCGGCTCGGGCACGGGCACTGTGTGCCAGAGGATCGCCCAGAACTTTGGCTTCCAGGATCTCTCCAGCGGGCACTT
CTTGCGGGAGAACATCAAGGCCAACACCGAAATTGGTGAGATGGCAAAACAGTATATAGAAAAAAGTCTTTTGGTTCCAG
ACCATATGATCACACGCCTAATGATGTCCGAGTTAGAGAATAGGCGTGGCCAGCACTGGCTCCTCCATGGGTTTCCTAGG
ACATTACGACAAGCCGAAGCGCTGGACAAGAATCTGTGACGTGGATCTAGTAATCAGTTTGAAGATTCCATTTGAAACAC
TTAAACATCGTCTCAGCTGCTGTTGGATTCACCCTCCTGGCGGAAGGGTATATAACATGGACTTCAATCCACCTCATATA
CATGGGATTGATGACGTCGCTGGTGAACCATTAGTCCAGTAGGAGGATGATAAACCTGAAGCAGTTGCTGCCAGGCTAAG
ACAG

Alignment

ORF - retro_mmul_2080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.65 %
• Parental protein coverage: 72.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPGSGKGTVCQRIAQNFGLQHLSSGHFLRENIKANTEVGEMAKQYIERSLLVPDHVITRLMMSELENRRG
          P.GSG.GTVCQRIAQNFG.Q.LSSGHFLRENIKANTE.GEMAKQYIE.SLLVPDH.ITRLMMSELENRRG
Retrocopy PTGSGTGTVCQRIAQNFGFQDLSSGHFLRENIKANTEIGEMAKQYIEKSLLVPDHMITRLMMSELENRRG

Parental  QHWLLDGFPRTLGQAEALDK-ICEVDLVISLNIPFETLKDRLSRRWIHPPSGRVYNLDFNPPHVHGIDDV
          QHWLL.GFPRTL.QAEALDK.IC.VDLVISL.IPFETLK.RLS..WIHPP.GRVYN.DFNPPH.HGIDDV
Retrocopy QHWLLHGFPRTLRQAEALDK>ICDVDLVISLKIPFETLKHRLSCCWIHPPGGRVYNMDFNPPHIHGIDDV

Parental  TGEPLVQQEDDKPEAVAARLRQ
          .GEPLVQ.EDDKPEAVAARLRQ
Retrocopy AGEPLVQ*EDDKPEAVAARLRQ

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	6.05 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.60 RPM
SRP007412_cerebellum	0.00 RPM	8.59 RPM
SRP007412_heart	0.00 RPM	6.65 RPM
SRP007412_kidney	0.00 RPM	57.98 RPM
SRP007412_liver	0.00 RPM	16.07 RPM
SRP007412_testis	0.38 RPM	0.53 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2080 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2080 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2080 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3320
Pan troglodytes	retro_ptro_2154
Gorilla gorilla	retro_ggor_1301
Pongo abelii	retro_pabe_2735

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014969	1 retrocopy	retro_amel_728,
Bos taurus	ENSBTAG00000030674	1 retrocopy	retro_btau_782,
Callithrix jacchus	ENSCJAG00000016835	1 retrocopy	retro_cjac_1856,
Homo sapiens	ENSG00000162433	6 retrocopies	retro_hsap_1101, retro_hsap_1744, retro_hsap_2993, retro_hsap_3320, retro_hsap_3619, retro_hsap_4225,
Gorilla gorilla	ENSGGOG00000026644	4 retrocopies	retro_ggor_1301, retro_ggor_2073, retro_ggor_2444, retro_ggor_2829,
Myotis lucifugus	ENSMLUG00000009622	1 retrocopy	retro_mluc_1708,
Macaca mulatta	ENSMMUG00000000143	2 retrocopies	retro_mmul_2032, retro_mmul_898,
Macaca mulatta	ENSMMUG00000001079	3 retrocopies	retro_mmul_104, retro_mmul_1680, retro_mmul_2080 ,
Mus musculus	ENSMUSG00000028527	1 retrocopy	retro_mmus_1933,
Nomascus leucogenys	ENSNLEG00000015163	3 retrocopies	retro_nleu_1666, retro_nleu_2481, retro_nleu_743,
Otolemur garnettii	ENSOGAG00000016024	1 retrocopy	retro_ogar_3375,
Ochotona princeps	ENSOPRG00000010345	17 retrocopies	retro_opri_1094, retro_opri_153, retro_opri_291, retro_opri_328, retro_opri_357, retro_opri_417, retro_opri_438, retro_opri_442, retro_opri_666, retro_opri_724, retro_opri_73, retro_opri_743, retro_opri_752, retro_opri_765, retro_opri_889, retro_opri_892, retro_opri_947,
Pongo abelii	ENSPPYG00000001269	6 retrocopies	retro_pabe_1021, retro_pabe_2479, retro_pabe_2735, retro_pabe_2970, retro_pabe_3412, retro_pabe_3483,
Pan troglodytes	ENSPTRG00000000827	4 retrocopies	retro_ptro_2024, retro_ptro_2154, retro_ptro_2449, retro_ptro_2870,