RetrogeneDB ID: retro_mmul_403

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:111958457..111958907(+)
• Located in intron of: ENSMMUG00000000390

Retrocopy information

• Ensembl ID: ENSMMUG00000031892
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COQ4
• Ensembl ID: ENSMMUG00000014147
• Aliases: None
• Description: None

Sequence

>retro_mmul_403
CAGAGCCTGCCAGAAGGCTCCCTGGGTCGCGAGTATCTCCGTTTCCTGGATGTGAATAGGGTCTCCCCAGACACCCGAGC
ACCCACCCGCTTCGTGGATGATGAGGAGCTAGCGTATGTGATTCAGCGATACCGGGAGGTGCACGACATGCTTCACACCC
TGCTGGGGATGCCCACCAACATCCTGGGGGAGATGGTGGTGAAATGGTATGAGGCTGTCCAGACTGGTCTGCCCATGTGC
ATCCTGGGTGCTCTCTTTGGACCGATCCAACTCAGTACTCAGAGCCTGCAAGTGCTGGTCTCGGAGTTGATCCCATGGGC
CGTTCAGAACGGGCGCACAGCCCCATGTGTCTTCAACCTGTACTATGAGCGGCGCTGGGAGCAGTCCCTGAGGGCTCTAC
GGGAGGAGCTGGGCATTGCGGCACCACCCGTGCATATCCAGGGCTTGGCC

Alignment

ORF - retro_mmul_403 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.67 %
• Parental protein coverage: 61.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QSLPEGSLGREYLRFLDVNRVSPDTRAPTRFVDDEELAYVIQRYREVHDMLHTLLGMPTNILGEIVVKWF
          QSLPEGSLGREYLRFLDVNRVSPDTRAPTRFVDDEELAYVIQRYREVHDMLHTLLGMPTNILGE.VVKW.
Retrocopy QSLPEGSLGREYLRFLDVNRVSPDTRAPTRFVDDEELAYVIQRYREVHDMLHTLLGMPTNILGEMVVKWY

Parental  EAVQTGLPMCILGALFGPIQLSAH-LQVLVSELIPWAVQNGRRAPCVLNLYYERRWEQSLRALREELGIT
          EAVQTGLPMCILGALFGPIQLS...LQVLVSELIPWAVQNGR.APCV.NLYYERRWEQSLRALREELGI.
Retrocopy EAVQTGLPMCILGALFGPIQLSTQSLQVLVSELIPWAVQNGRTAPCVFNLYYERRWEQSLRALREELGIA

Parental  APPVHIQGLA
          APPVHIQGLA
Retrocopy APPVHIQGLA

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	1.12 RPM	4.59 RPM
SRP007412_brain_prefrontal_cortex	1.75 RPM	15.79 RPM
SRP007412_cerebellum	1.03 RPM	6.01 RPM
SRP007412_heart	0.65 RPM	3.89 RPM
SRP007412_kidney	1.64 RPM	11.27 RPM
SRP007412_liver	2.45 RPM	19.32 RPM
SRP007412_testis	1.47 RPM	8.37 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_403 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_403 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_403 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000014147	1 retrocopy	retro_mmul_403 ,