RetrogeneDB ID: retro_mmul_2537

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:128890458..128890829(+)
• Located in intron of: ENSMMUG00000013162

Retrocopy information

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

Parental gene information

• Parental gene symbol: C12orf49
• Ensembl ID: ENSMMUG00000018247
• Aliases: None
• Description: chromosome 12 open reading frame 49 [Source:HGNC Symbol;Acc:26128]

Sequence

>retro_mmul_2537
ATGGTGAACCTGGCGGCCATGGTGTGGCGCCGGCTTCTGCGGAAGAAGTGGGTTCTCGCCCTGGTCTTTGGGCTGCGCTT
GTCTACTTCCTCAGCAGCACCTCCAAGCAGGAGGAGAGGGCAGTGAGGGATGGAAATTCCCCTGCAGGTTCAAGACCATG
ATCAGCCCATCCCGTGGAAAGTGCAGTTTAACTTCGGCAATAGCAGTCCTCCCAGCAATCAGTGCCGCAACCCCATTAAA
GGGAAACACCTCATCACAGATGAACTCAGCTACGTTTGTGAGAGGAAGGATTGCTGGTGAATGGCTGCTGTAACGTCAAC
GTCTCTAGCACAAAGCAGTACTGCAGCGATGGCTGCTGGTCAAATGGCTGC

Alignment

ORF - retro_mmul_2537 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.83 %
• Parental protein coverage: 60.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVNLAAMVWRRLLRKRWVLALVFGL-SLVYFLSSTFKQEERAVRDRNL-LQVHDHNQPIPWKVQFNLGNS
          MVNLAAMVWRRLLRK.WVLALVFGL..LVYFLSST.KQEERAVRD.N..LQV.DH.QPIPWKVQFN.GNS
Retrocopy MVNLAAMVWRRLLRKKWVLALVFGL<ALVYFLSSTSKQEERAVRDGNS>LQVQDHDQPIPWKVQFNFGNS

Parental  SRPSNQCRNSIQGKHLITDELGYVCERKD-LLVNGCCNVNVPSTKQYCCDGCWPNGC
          S.PSNQCRN.I.GKHLITDEL.YVCERKD.LLVNGCCNVNV.STKQYC.DGCW.NGC
Retrocopy SPPSNQCRNPIKGKHLITDELSYVCERKD<LLVNGCCNVNVSSTKQYCSDGCWSNGC

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	5.83 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	15.23 RPM
SRP007412_cerebellum	0.00 RPM	5.62 RPM
SRP007412_heart	0.00 RPM	4.00 RPM
SRP007412_kidney	0.00 RPM	6.46 RPM
SRP007412_liver	0.00 RPM	3.17 RPM
SRP007412_testis	0.00 RPM	18.81 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2537 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2537 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2537 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4758
Gorilla gorilla	retro_ggor_2963

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012481	2 retrocopies	retro_amel_1518, retro_amel_1578,
Bos taurus	ENSBTAG00000047139	1 retrocopy	retro_btau_1667,
Callithrix jacchus	ENSCJAG00000009570	1 retrocopy	retro_cjac_1471,
Dasypus novemcinctus	ENSDNOG00000001294	9 retrocopies	retro_dnov_126, retro_dnov_1532, retro_dnov_1609, retro_dnov_1622, retro_dnov_1739, retro_dnov_2042, retro_dnov_2185, retro_dnov_2285, retro_dnov_232,
Echinops telfairi	ENSETEG00000016892	3 retrocopies	retro_etel_1064, retro_etel_1377, retro_etel_410,
Homo sapiens	ENSG00000111412	1 retrocopy	retro_hsap_4758,
Gorilla gorilla	ENSGGOG00000015690	2 retrocopies	retro_ggor_2963, retro_ggor_508,
Myotis lucifugus	ENSMLUG00000011912	1 retrocopy	retro_mluc_166,
Macaca mulatta	ENSMMUG00000018247	2 retrocopies	retro_mmul_2376, retro_mmul_2537 ,
Pan troglodytes	ENSPTRG00000005500	1 retrocopy	retro_ptro_2798,