RetrogeneDB ID: retro_mmul_2376

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:146386217..146386528(-)
• Located in intron of: None

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_2376
TGGGCATGTGGGGCCCTTGCCCAGGCTATCCTCGTCCATGTCCTCAGCAGCACCTTCAGGCGGGAAGAGAGGGAGTGAGA
CATAGGACTCTCCTCCAGGCTCAAGACCATGACCAGCCCAGCCCATGGAAAGTGCAGGTTAACCTGGGCAGTAGCAGTTG
CCTGAGCAATCAGGGCTGGAACTCTGTTCAAGGGAAGCGCCTCATCATGGATGAACCAGGCTATGTTTGTGAGAGGAGGG
ATTTGCTGGTGAAGGACTGTAACCTCCACATCCCTAGTGTGAAGCAGTACTGCTGTGATGGCTGCTGGCCA

Alignment

ORF - retro_mmul_2376 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.21 %
• Parental protein coverage: 51.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WVLALVFGLSLVYFLSSTFKQEER-AVRDRNLLQVHDHNQPIPWKVQFNLGNSSRPSNQCRNSIQGKHLI
          W.........LV..LSSTF..EER..VR.R.LLQ..DH.QP.PWKVQ.NLG.SS..SNQ..NS.QGK.LI
Retrocopy WACGALAQAILVHVLSSTFRREER<GVRHRTLLQAQDHDQPSPWKVQVNLGSSSCLSNQGWNSVQGKRLI

Parental  TDELGYVCERKDLLVNGCCNVNVPSTKQYCCDGCWP
          .DE.GYVCER.DLLV...CN...PS.KQYCCDGCWP
Retrocopy MDEPGYVCERRDLLVKD-CNLHIPSVKQYCCDGCWP

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	0.08 RPM	15.23 RPM
SRP007412_cerebellum	0.00 RPM	5.62 RPM
SRP007412_heart	0.06 RPM	4.00 RPM
SRP007412_kidney	0.00 RPM	6.46 RPM
SRP007412_liver	0.00 RPM	3.17 RPM
SRP007412_testis	0.15 RPM	18.81 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2376 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2376 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2376 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2798
Callithrix jacchus	retro_cjac_1471

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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,