RetrogeneDB ID: retro_mmul_1207

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:107234960..107235320(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000016109
• Aliases: None
• Description: None

Sequence

>retro_mmul_1207
CCATCCAGCTGCCTGACTGCCTCTTCGCCTCTCCCGCGGGAACTCCAGCGTCTCCTTGGCTCGAAATGGACCCCACGGTT
CCAGCACCACTGGCAGCTCCTGCACCTGTGCTGGCTCCTGCAAATGCAAAGAGTGCAAATGCACCTCGTGCAAGAAGAGC
TGCTCCTGCTGCCCCGGGGGCTGTGCCAGCTGTGCCCAGGGCTGCATCTGCAAAGGGGCGTCGGAGAAATGCAGCTGCTG
TGCCTGGTGTGGGGACAGCCCTGCTCCCAGATGTAAATGAAGCAACATGGGTACAAACCTGGATTTTTTTTTTCATACAA
CCCTGAGCCATTTGCTACATTCCTTTTTCTATTAAATATG

Alignment

ORF - retro_mmul_1207 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.36 %
• Parental protein coverage: 87.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PSSCLTPSSPLPSS----LGWKWTP-TAPAPLEPPAPVPAPASAKSANAPRARRAAAPAAPWAVPSVPRA
          PSSCLT.SSPLP......LG.KWTP.T.PAPL..PAPV.APA.AKSANAPRARRAA.PAAP.AVP.VPRA
Retrocopy PSSCLTASSPLPRELQRLLGSKWTP<TVPAPLAAPAPVLAPANAKSANAPRARRAA-PAAPGAVPAVPRA

Parental  ASAKGHRRSAAAVPDVGTALLPDVNRATCTNLDFFFLYNP-EPFATFVFLLNM
          ASAKG.RR.AAAVP.VGTALLPDVN.AT...........P.EPFATF.FLLNM
Retrocopy ASAKGRRRNAAAVPGVGTALLPDVNEATWVQTWXXXXIQP>EPFATFLFLLNM

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	0.45 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.24 RPM
SRP007412_cerebellum	0.00 RPM	0.19 RPM
SRP007412_heart	0.06 RPM	0.29 RPM
SRP007412_kidney	0.00 RPM	3.05 RPM
SRP007412_liver	0.00 RPM	0.71 RPM
SRP007412_testis	0.04 RPM	0.00 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1207 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1207 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1207 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000016109	2 retrocopies	retro_mmul_1207 , retro_mmul_2513,
Procavia capensis	ENSPCAG00000007865	1 retrocopy	retro_pcap_77,
Pteropus vampyrus	ENSPVAG00000016198	1 retrocopy	retro_pvam_245,