RetrogeneDB ID: retro_mmul_540

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:150143049..150143297(-)
• Located in intron of: ENSMMUG00000007784

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4321
• Ensembl ID: ENSMMUG00000005759
• Aliases: None
• Description: gamma-aminobutyric acid receptor-associated protein-like 2 [Source:RefSeq peptide;Acc:NP_001181193]

Sequence

>retro_mmul_540
GTGAAGTGGGTGTTCAGAGAGGACTGCTCCTGGAACACAGGTGAGTGGAGTCCCCAAAGATCCATGCAAAACAGCCCGGC
CGGTTCCAGCAATTATGAAAAAGTCCAGGCTCTCAGACCGCTGACCCTGATAAGTAGATGTCCTTGGTGCCACCTGGTAT
TGTAGTGACTCAGTCCATGTGCATCATCACCAGTAGGATCCAGCTTCCTGCTGAAAAGCCCTCTGTCCCGTTTGTGGATA
AGACAGTG

Alignment

ORF - retro_mmul_540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.23 %
• Parental protein coverage: 71.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MKWMFKEDHS-LEHRCVESAKIRAKYPDR-VPVIV-EKVS-GSQIVDIDKRKYLVPSDITVAQFMWIIRK
          .KW.F.ED.S.LEHR.VES.KI.AK.P.R.VP.I..EKV..GSQ..D.DK...LVP..I.V.Q.M.II..
Retrocopy VKWVFREDCS<LEHR*VESPKIHAKQPGR<VPAIM<EKVQ<GSQTADPDK*MSLVPPGIVVTQSMCIITS

Parental  RIQLPSEKAIFLFVDKTV
          RIQLP.EK....FVDKTV
Retrocopy RIQLPAEKPSVPFVDKTV

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	84.71 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	90.59 RPM
SRP007412_cerebellum	0.00 RPM	106.35 RPM
SRP007412_heart	0.00 RPM	58.00 RPM
SRP007412_kidney	0.00 RPM	50.82 RPM
SRP007412_liver	0.00 RPM	22.17 RPM
SRP007412_testis	0.04 RPM	26.05 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_540 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_540 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_342
Pongo abelii	retro_pabe_372

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005453	2 retrocopies	retro_amel_1054, retro_amel_1238,
Callithrix jacchus	ENSCJAG00000014253	1 retrocopy	retro_cjac_146,
Dasypus novemcinctus	ENSDNOG00000002240	2 retrocopies	retro_dnov_1755, retro_dnov_2332,
Homo sapiens	ENSG00000034713	1 retrocopy	retro_hsap_4115,
Gorilla gorilla	ENSGGOG00000012299	2 retrocopies	retro_ggor_2761, retro_ggor_342,
Loxodonta africana	ENSLAFG00000017065	2 retrocopies	retro_lafr_234, retro_lafr_543,
Myotis lucifugus	ENSMLUG00000015112	1 retrocopy	retro_mluc_1207,
Macaca mulatta	ENSMMUG00000002197	1 retrocopy	retro_mmul_2235,
Macaca mulatta	ENSMMUG00000005759	2 retrocopies	retro_mmul_2369, retro_mmul_540 ,
Macaca mulatta	ENSMMUG00000010545	1 retrocopy	retro_mmul_155,
Macaca mulatta	ENSMMUG00000017613	1 retrocopy	retro_mmul_15,
Nomascus leucogenys	ENSNLEG00000013048	2 retrocopies	retro_nleu_1560, retro_nleu_580,
Pongo abelii	ENSPPYG00000007565	2 retrocopies	retro_pabe_3368, retro_pabe_372,
Pan troglodytes	ENSPTRG00000008362	2 retrocopies	retro_ptro_250, retro_ptro_2794,
Rattus norvegicus	ENSRNOG00000019425	1 retrocopy	retro_rnor_57,