RetrogeneDB ID: retro_mmul_393

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:95111360..95112129(+)
• Located in intron of: ENSMMUG00000002199

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.681
• Ensembl ID: ENSMMUG00000002194
• Aliases: None
• Description: None

Sequence

>retro_mmul_393
TCTTTAGCTAAAGCCATTGAAAAGAATGTGCTGATTTCACATCTTGATGATAATGAGAGAAGTGATATTTTTGATGCCAT
GTTTCCAGTCTCCTTTATCACTGGAGAGACAGTGATTCTGCAAGGTGATGAAGGGGATAACTTCTGTGTGATTGATCAAG
GAGAGAGGGATGTCTGTGTCAATGATGAATGAGCAACCAGTATTGAGGAAGGAGGGAGCTTTGGAGAATTTGTTTTGATT
TATGGAACACCTAGAGTAGCCACTGTCAAAGCAAAGGCAAATGTGAAATGGTAGTGTATCAACCGAGACAGCTATGGAAG
AATCTGTATGGGAAGCACACTGAGAAAGTGGAAGATGTATGAGGAATTCTTTAGTAAAGTGTCTATTTTAGAGTCTCTGG
ATAAGAGGGAGCATCTTATGGTAGCCGATACATGGGAACCAGTCAAGTTTGAAGACTGGCAGAAGATTGTGGTGCAGGGA
GAACCAGGGGATGAGAGGTGAGTTCCTTATTATTCTAGAGGGGCCAGCTGCTATGCTGCAATGTTGGTCAGAAAATGAAG
AGTTTGTTGAAGTGGGAAGATCGGAGCCTTCTGATTATTTTGGTGAACTTGCATTACTGATGAATCATCCTCCTGCTGCC
ACAGTGGTTGTACATGGCCCCTTGAAGTACATTAAGCTGGACCAGCCTAGATCTGAATGTGCTCTTGGCTCATGCTCAGA
CCTCCTCAAACGAAACATCTAGTAGTACAACAGTTTTGTGTCACTGTCT

Alignment

ORF - retro_mmul_393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.71 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALAKAIEKNVLFSHLDDNERSDIFDAMFSVSFIAGETVIQQGDEGDNFYVIDQGETDVYVNNEWATSVGE
          .LAKAIEKNVL.SHLDDNERSDIFDAMF.VSFI.GETVI.QGDEGDNF.VIDQGE.DV.VN.E.ATS..E
Retrocopy SLAKAIEKNVLISHLDDNERSDIFDAMFPVSFITGETVILQGDEGDNFCVIDQGERDVCVNDE*ATSIEE

Parental  GGSFGELALIYGTPRAATVKAKTNVKLWGIDRDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERLT
          GGSFGE..LIYGTPR.ATVKAK.NVK...I.RDSY.RI.MGSTLRK.KMYEEF.SKVSILESLDK.E.L.
Retrocopy GGSFGEFVLIYGTPRVATVKAKANVKW*CINRDSYGRICMGSTLRKWKMYEEFFSKVSILESLDKREHLM

Parental  VADALEPVQFED-GQKIVVQGEPG--DEFFIILEGSAAVLQRRSENEEFVEVGRLGPSDYFGEIALLMNR
          VAD..EPV.FED.G.........G...EF.IILEG.AA.LQ..SENEEFVEVGR..PSDYFGE.ALLMN.
Retrocopy VADTWEPVKFED>GRRLWCRENQGMRGEFLIILEGPAAMLQCWSENEEFVEVGRSEPSDYFGELALLMNH

Parental  PRAATVVARGPLKCVKLDRPRFERVLGPCSDILKRNIQQYNSFVSLS
          P.AATVV..GPLK..KLD.PR.E..LG.CSD.LKRNI..YNSFVSLS
Retrocopy PPAATVVVHGPLKYIKLDQPRSECALGSCSDLLKRNI**YNSFVSLS

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	0.11 RPM	388.70 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	338.34 RPM
SRP007412_cerebellum	0.06 RPM	316.29 RPM
SRP007412_heart	0.00 RPM	353.02 RPM
SRP007412_kidney	0.00 RPM	229.81 RPM
SRP007412_liver	0.00 RPM	76.91 RPM
SRP007412_testis	0.04 RPM	235.40 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_393 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_393 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_393 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_186

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000108946	1 retrocopy	retro_hsap_186,
Gorilla gorilla	ENSGGOG00000016507	1 retrocopy	retro_ggor_267,
Macaca mulatta	ENSMMUG00000002194	2 retrocopies	retro_mmul_2498, retro_mmul_393 ,
Nomascus leucogenys	ENSNLEG00000001982	1 retrocopy	retro_nleu_996,
Pan troglodytes	ENSPTRG00000009579	1 retrocopy	retro_ptro_172,
Ictidomys tridecemlineatus	ENSSTOG00000012903	1 retrocopy	retro_itri_104,