RetrogeneDB ID: retro_mmul_1995

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:29037456..29038227(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1802
• Ensembl ID: ENSMMUG00000009693
• Aliases: None
• Description: succinyl-CoA ligase [Source:RefSeq peptide;Acc:NP_001248050]

Sequence

>retro_mmul_1995
CAGTCACTTCAATTAACTTCCTGAAGATGGCAGACCCTCCAGGAACACCAGAGCAAGAAACTGATGTCTGACAACAGAGT
GAGAGTTCAAATATTCTTTGTAGCAGACACTGTGAATGAAGCACTTGAAGTTGCCAAGAGACTAAAAGCAAAATAAATTG
TTTTAATTAAAAGCCCAGATCTTAGCTGGAGGAAAAGGAAAGGGTGTCTTCAACTGTGGTTTGAAACGAAGTGTTCACTT
AACAAAAGATCCTAAAGTTGTGGGAAAGCTGGCTAAACATGATTGGGTATGTTTGGGGCAATAAACCAAACTCCAAAAGA
AGATGTGAAAGTTAACAAGCTGATGGTTACTGAAACCTTGGACACTTCCAGAAAAACTTACCTGGTGATCCTGATAGACA
GGTCCTGCCATGGCCCCATGCTGGTGGGCAGGCCCCAGGGGCCATTGACATTGAAGAGGTGGATGCTTCAAATTCAGAAT
TTATTTTTAAGGAGCAAATTTTTCAAGGGATAAAGGACAGCCGAGTTCAGAGTTCAGCAGATGGCAGAAAATCTAGGCTT
CCTTGGGTCTTTGAAAAACCAGGTTGCAGATCAAATTAAGAAACTGTATAATCTCTTCCTAAAAATTGATGCTACTCAGG
TGATAGTGAATCCCTCTGGTGAAATCTGAGAAAGACAAGTTGTCTGCTTTAATGCGAACATAAACTTTCATGACAATGCA
GGATTCTAACAACAGGACATATCTGCTATGGATGACAAATCGGAGAATGAG

Alignment

ORF - retro_mmul_1995 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.59 %
• Parental protein coverage: 59.26 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QAAQLTSRRWLNLQEYQSKKLMSDNGVRVQRFFVADTANEALEAAKRLNAKEIVL-KAQILAGGRGKGVF
          Q..QLTS.RW..LQE.QSKKLMSDN.VRVQ.FFVADT.NEALE.AKRL.AK.IVL.K...L.....KG..
Retrocopy QSLQLTS*RWQTLQEHQSKKLMSDNRVRVQIFFVADTVNEALEVAKRLKAK*IVLIKSPDLSWRKRKGCL

Parental  NSGLKGGVHLTKDPNVVGQLAKQMIGYNLATKQTPKEGVKVNKVMVAEALDISRETYLAILMDRSCNGPV
          .........L.K.....G.......G...A..QTPKE.VKVNK.MV.E.LD.SR.TYL.IL.DRSC.GP.
Retrocopy QLWFETKCSLNKRS*SCGKAG*T*LGMFGAINQTPKEDVKVNKLMVTETLDTSRKTYLVILIDRSCHGPM

Parental  LVGSPQGGVDIEEVAASNPELIFKEQIDIFEGIKDSQAQRMAENLGFVGPLKSQAADQITKLYNLFLKID
          LVG.PQG.............L.................Q.MAENLGF.G.LK.Q.ADQI.KLYNLFLKID
Retrocopy LVGRPQGPLTLKRWMLQIQNLFLRSKFFKG*RTAEFRVQQMAENLGFLGSLKNQVADQIKKLYNLFLKID

Parental  ATQVEVNPFGETPEGQVVCFDAKINFDDNAEFRQKDIFAMDDKSENE
          ATQV.VNP.GE..E.QVVCF.A.INF.DNA.F.Q.DI.AMDDKSENE
Retrocopy ATQVIVNPSGEI*ERQVVCFNANINFHDNAGF*QQDISAMDDKSENE

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	11.32 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.49 RPM
SRP007412_cerebellum	0.00 RPM	8.33 RPM
SRP007412_heart	0.00 RPM	72.43 RPM
SRP007412_kidney	0.00 RPM	181.10 RPM
SRP007412_liver	0.00 RPM	111.31 RPM
SRP007412_testis	0.00 RPM	12.06 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1995 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1995 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1995 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2624

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000172340	1 retrocopy	retro_hsap_1044,
Gorilla gorilla	ENSGGOG00000027438	1 retrocopy	retro_ggor_825,
Myotis lucifugus	ENSMLUG00000017294	1 retrocopy	retro_mluc_695,
Macaca mulatta	ENSMMUG00000007539	1 retrocopy	retro_mmul_1231,
Macaca mulatta	ENSMMUG00000009693	2 retrocopies	retro_mmul_1273, retro_mmul_1995 ,
Mus musculus	ENSMUSG00000061838	1 retrocopy	retro_mmus_3720,
Nomascus leucogenys	ENSNLEG00000007553	1 retrocopy	retro_nleu_915,
Otolemur garnettii	ENSOGAG00000006190	1 retrocopy	retro_ogar_161,
Pongo abelii	ENSPPYG00000013735	1 retrocopy	retro_pabe_2624,
Pteropus vampyrus	ENSPVAG00000004554	1 retrocopy	retro_pvam_912,