RetrogeneDB ID: retro_mmul_2510

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:80011764..80012391(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.12143
• Ensembl ID: ENSMMUG00000011360
• Aliases: None
• Description: None

Sequence

>retro_mmul_2510
TTTGAAGAACTCAGCAAACTAATGATCAAGGCTAAGGAAATGGTGGAGTTATCAAAATCAATTGCTAATAAAATTAAAGA
CAAACAAGGTGACATCACAGAAGATGAGACCATCAGGTTTAAATCCTACTTGCTGAGCATGGGAATAGCTAACCCAGTTA
CCAGAGAAACCTACGGCTCAGGCACACAGTACCACATGCAATTGGCCAAACAGCTGGCTGGAATATTGCAGGTGCCTTTA
GAGGAATGAGGGGGAATAATGTCACTCACGGAGGTGTACTGCTTAGTAAACCGAGCTCGAGGAATGGAATTACTCTCACC
AGAAGATTTAGTGAATGCGTGCAAGATGCTGGAAGCACTGAAATTACCTCTCAGGCTCCGTGTGTTTGACAGTGGCGTCA
TGGTAATTGAGCTTCAGTCTCACAAGGAAGAGGAAATGGTGGCCTAGGCCCTGGAGACAGTTTCAGAAAAGGGATCCCTA
ACATCGGAAGAGTTTGCTAAGCTTGTGGGAATGTCTGTCCTTCTAGCCAAAGAAAGGTTGCTGCTTGCAGAGAAGATGGG
CCGTCTTTGCCGTGATGACTCAGTGAAAGGCCTGCGTTTTTACCCAAGTTTATTTATGACACAGAGC

Alignment

ORF - retro_mmul_2510 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.13 %
• Parental protein coverage: 54.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FEDLSKLMIKAKEMVELSKSIANKIKDKQGDITEDETIRFKSYLLSMGIANPVTRETYGSGTQYHMQLAK
          FE.LSKLMIKAKEMVELSKSIANKIKDKQGDITEDETIRFKSYLLSMGIANPVTRETYGSGTQYHMQLAK
Retrocopy FEELSKLMIKAKEMVELSKSIANKIKDKQGDITEDETIRFKSYLLSMGIANPVTRETYGSGTQYHMQLAK

Parental  QLAGILQVPLEERGGIMSLTEVYCLVNRARGMELLSPEDLVNACKMLEALKLPLRLRVFDSGVMVIELQS
          QLAGILQVPLEE.GGIMSLTEVYCLVNRARGMELLSPEDLVNACKMLEALKLPLRLRVFDSGVMVIELQS
Retrocopy QLAGILQVPLEE*GGIMSLTEVYCLVNRARGMELLSPEDLVNACKMLEALKLPLRLRVFDSGVMVIELQS

Parental  HKEEEMVASALETVSEKGSLTSEEFAKLVGMSVLLAKERLLLAEKMGHLCRDDSVEGLRFYPNLFMTQS
          HKEEEMVA.ALETVSEKGSLTSEEFAKLVGMSVLLAKERLLLAEKMG.LCRDDSV.GLRFYP.LFMTQS
Retrocopy HKEEEMVA*ALETVSEKGSLTSEEFAKLVGMSVLLAKERLLLAEKMGRLCRDDSVKGLRFYPSLFMTQS

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	0.45 RPM	46.39 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	33.87 RPM
SRP007412_cerebellum	0.52 RPM	63.61 RPM
SRP007412_heart	0.12 RPM	26.26 RPM
SRP007412_kidney	0.59 RPM	46.60 RPM
SRP007412_liver	0.20 RPM	20.27 RPM
SRP007412_testis	0.00 RPM	10.55 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2510 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2510 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2510 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008949	1 retrocopy	retro_chof_702,
Macaca mulatta	ENSMMUG00000011360	1 retrocopy	retro_mmul_2510 ,
Otolemur garnettii	ENSOGAG00000011312	1 retrocopy	retro_ogar_913,
Ictidomys tridecemlineatus	ENSSTOG00000004651	1 retrocopy	retro_itri_97,