RetrogeneDB ID: retro_mmul_2406

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:61722175..61722425(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGA1
• Ensembl ID: ENSMMUG00000019529
• Aliases: None
• Description: high mobility group protein HMG-I/HMG-Y [Source:RefSeq peptide;Acc:NP_001253281]

Sequence

>retro_mmul_2406
ATGAGAGGGTCCAGGTCGAAATCTAGCCAGCCCTGGGCCTCCAAGCAGGAAAAGGACTACACTGAGCAGGGGGGCCAGGG
CAGGCCGCAGGCAGCCTCCGCAGGAGCCCGGCCAACACCTGGGAGACCCGGGGCCACCAAAGGGCAGCAAAATCAGGGCC
GCTGCTGAGACCCGGAAACCCACCACAACTCCAGGAAGGAAACCAAGGGGCCGACCCAAAAAACTGGAAGGGAGGGAGGG
AGAGGAGGGC

Alignment

ORF - retro_mmul_2406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 89.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSESSSKSSQPLASKQEKDGTEKRGRGRP-RKQPPKEPSEVPTPKRPRGRPKGSKNKGAAKTRKTTTTPG
          M..S.SKSSQP.ASKQEKD.TE..G.GRP.R..P.........P....G.PKGSK...AA.TRK.TTTPG
Retrocopy MRGSRSKSSQPWASKQEKDYTEQGGQGRP>RQPPQEPGQHLGDP----GPPKGSKIRAAAETRKPTTTPG

Parental  RKPRGRPKKLE-KEEEEG
          RKPRGRPKKLE..E.EEG
Retrocopy RKPRGRPKKLEGREGEEG

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	12.33 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	40.14 RPM
SRP007412_cerebellum	0.00 RPM	11.69 RPM
SRP007412_heart	0.12 RPM	7.30 RPM
SRP007412_kidney	0.00 RPM	3.40 RPM
SRP007412_liver	0.00 RPM	4.28 RPM
SRP007412_testis	0.08 RPM	40.52 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2406 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2406 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_695
Pan troglodytes	retro_ptro_499

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001061	1 retrocopy	retro_amel_1637,
Callithrix jacchus	ENSCJAG00000015226	2 retrocopies	retro_cjac_1197, retro_cjac_3158,
Homo sapiens	ENSG00000137309	4 retrocopies	retro_hsap_1175, retro_hsap_2277, retro_hsap_4663, retro_hsap_695,
Myotis lucifugus	ENSMLUG00000010085	2 retrocopies	retro_mluc_1619, retro_mluc_2429,
Macaca mulatta	ENSMMUG00000019529	2 retrocopies	retro_mmul_1276, retro_mmul_2406 ,
Mus musculus	ENSMUSG00000046711	1 retrocopy	retro_mmus_188,
Nomascus leucogenys	ENSNLEG00000008303	1 retrocopy	retro_nleu_1097,
Procavia capensis	ENSPCAG00000016076	1 retrocopy	retro_pcap_236,
Pongo abelii	ENSPPYG00000029838	4 retrocopies	retro_pabe_1941, retro_pabe_2441, retro_pabe_3623, retro_pabe_960,
Pan troglodytes	ENSPTRG00000040884	6 retrocopies	retro_ptro_1611, retro_ptro_2053, retro_ptro_3098, retro_ptro_499, retro_ptro_789, retro_ptro_807,
Pteropus vampyrus	ENSPVAG00000014283	1 retrocopy	retro_pvam_116,
Rattus norvegicus	ENSRNOG00000000488	1 retrocopy	retro_rnor_164,