RetrogeneDB ID: retro_mmul_2493

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:51664805..51665356(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.18736
• Ensembl ID: ENSMMUG00000005025
• Aliases: None
• Description: mpv17-like protein 2 precursor [Source:RefSeq peptide;Acc:NP_001181564]

Sequence

>retro_mmul_2493
TGGCACTGGCTGCATGGCCTGTGGACTATGGGACAGTCCCTGTTGCATGGCTGTGTGCTGCTGGTCATCAATACACTGGG
CTGTGGTATGCTTATGGTGGCCCGGGACATTGCGTGACAGTCCTGGGAGGTCTACACCCAGCTGACCAGATGTTCCACAG
GTGGCACTCAGTGAGCATGTTTGCAGTGGATGGCAACGTGGATCCTTTCCCGCACTACTGGTACCTCTGTCTGGACTGCC
TACTCCCTGTGTCTGGCCTCTGTGGCCTCCCAAGTGCCCTCAGGAAGGTCCTCATGGATCAGCTGGTAGCCTCTCCCATG
CCGAGCATATGATACTTCTTGGGCCTTGGCTGCCTGGAAGGCCAGACACTGGGAGAGAGCTGCCAGGAGCTGCAGGACAA
GTTCTGGGAATTCTACAAGGCTGACTGGTGCATGTGGCCGGCTGCACGCTGGTGAACTTTCCCTTTGTGTACACCCCACT
CCCAGTTCCGAGTCACCTACATCAATGGCCTGACATTGGGCTGGGACACATATCTGTCCTACCTGAAGTAC

Alignment

ORF - retro_mmul_2493 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.24 %
• Parental protein coverage: 88.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WRRLRRLLSAGQLLFQGRALLVTNTLGCGALMAAGDGLRQSWEIRAR-PGQVFDPRRSASMFAVGCSMGP
          W..L..L...GQ.L..G..LLV.NTLGCG.LM.A.D...QSWE.......Q.F....S.SMFAV.....P
Retrocopy WHWLHGLWTMGQSLLHGCVLLVINTLGCGMLMVARDIA*QSWEVYTQ<ADQMFHRWHSVSMFAVDGNVDP

Parental  FLHYWYLSLDRLFPASGLRGFPNVLKKVLVDQLVASPLLGVWYFLGLGCMEGQTVGESCQELREKFWEFY
          F.HYWYL.LD.L.P.SGL.G.P..L.KVL.DQLVASP.....YFLGLGC.EGQT.GESCQEL..KFWEFY
Retrocopy FPHYWYLCLDCLLPVSGLCGLPSALRKVLMDQLVASPMPSI*YFLGLGCLEGQTLGESCQELQDKFWEFY

Parental  KADWCVWPAAQFVNFLFVPP--QFRVTYINGLTLGWDTYLSYLKY
          KADWC.WPAA....F....P..QFRVTYINGLTLGWDTYLSYLKY
Retrocopy KADWCMWPAARW*TFPLCTPHSQFRVTYINGLTLGWDTYLSYLKY

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	37.99 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	73.62 RPM
SRP007412_cerebellum	0.00 RPM	18.15 RPM
SRP007412_heart	0.00 RPM	7.71 RPM
SRP007412_kidney	0.00 RPM	10.92 RPM
SRP007412_liver	0.00 RPM	9.82 RPM
SRP007412_testis	0.00 RPM	5.35 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2493 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2493 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2493 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_4063

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000027644	1 retrocopy	retro_acar_180,
Bos taurus	ENSBTAG00000025788	1 retrocopy	retro_btau_306,
Callithrix jacchus	ENSCJAG00000014104	1 retrocopy	retro_cjac_4063,
Echinops telfairi	ENSETEG00000013840	1 retrocopy	retro_etel_1446,
Macropus eugenii	ENSMEUG00000016379	2 retrocopies	retro_meug_223, retro_meug_943,
Macaca mulatta	ENSMMUG00000005025	1 retrocopy	retro_mmul_2493 ,
Nomascus leucogenys	ENSNLEG00000005944	1 retrocopy	retro_nleu_2666,
Pteropus vampyrus	ENSPVAG00000002028	1 retrocopy	retro_pvam_1254,