RetrogeneDB ID: retro_mmul_1843

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:84535183..84536465(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000029540
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.10035
• Ensembl ID: ENSMMUG00000012575
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein Q [Source:RefSeq peptide;Acc:NP_001180774]

Sequence

>retro_mmul_1843
ATGGCTACAGAACATGTTAATGGAAATGGTACTGAAGAGCCCATGGATACTACTTCTGCAGTTATCCATTCAGAAAATTT
TCAGACATTGCCTGATGCTGGTTTACCACAGAAAGTTGCTGAAAAACTAGATGAAATTTACGTTGCAGGGCTAGTTGCAC
ATAGTGATTTAGATGAAAGAGCTATTGAAGCTTTAAAAGAATTCAATGAAGACGGTGCATTGGCAGTTCTTCAACAGTTT
AAAGACAGTGATCTCTCTCATGTTCAGAACAAAAGTGCCTTTTTATGTGGAGTCATGAAGACTTATAGGCAGAGAGAAAA
ACAAGGGACCAAAGTAGCAGACTCTAGTAAAGGACCAGATGAGGCAAAAATTAAGGCACTCTTGGAAAGAACAGGCTACA
TACTTGATGTGACCACTGGACAGAGGAAGTATGGGGGACCACCTCCAGATTCCGTTTATTCAGGTCAGCAGCCTTCTGTT
GGCACTGAGATATTTGTGGGAAAGATCCCAAGAGATCTATTTGAGGATGAACTTGTTCCTTTATTTGAGAAAGCTGGACC
TATATGGGATCTTCGTCTAATGATGGATCCACTCACTGGTCTCAATAGAGGTTATGCGTTTGTCACTTTCTGTACAAAAG
AAGCAGCTCAGGAGGCTGTTAAACTGTATAATAATCATGAAACTCGTTCTGGAAAACACATTGGTGTCTGCATCTCGGTT
GCCAACAATAGGCTTTTTGTGGGCTCTATTCCTAAGAGTAAAACCAAGGAACAGATTCTTGAAGAATTTAGCAAAGTAAC
AGAGGGTCTTACAGACGTCATTTTATACCACCAACCGGATGACAAGAAAAAAAAACAGAGGCTTTTGCTTTCTTGAATAT
GAAGATCACAAAACAGCTGCCCAGGCAAGGCGTAGGTTAATGAGTGGTAAAGTCAAGGTCTGGGGGAATGTTGGAACTGT
TGAATGGGCTGATCCTATAGAAGATCCTGATCCTGAGGTTATGGCAAAGGTAAAAGTGCTGTTTGTACGCAACCTTGCCA
ATACTGTAACAGAAGAGATTTTAGAAAAGGCATTTAGTCAGTTTGGGAAACTGGAACGAGTGAAGAAGTTAAAAGATTAT
GCATTCATTCATTTTGATGAACGAGATGGTGCTGTCAAGGCTATGGAAGAAATGAATGGCAAAGACTTGGAGGGAGAAAA
TATTGAAATTGTTTTTGCCAAGCCACCAGATCAGAAAAGGAAAGAAAGAAAAGCTCAGAGGCAAGCAGCAAAAAATCAAA
TG

Alignment

ORF - retro_mmul_1843 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.36 %
• Parental protein coverage: 75.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATEHVNGNGTEEPMDTTSAVIHSENFQTLLDAGLPQKVAEKLDEIYVAGLVAHSDLDERAIEALKEFNE
          MATEHVNGNGTEEPMDTTSAVIHSENFQTL.DAGLPQKVAEKLDEIYVAGLVAHSDLDERAIEALKEFNE
Retrocopy MATEHVNGNGTEEPMDTTSAVIHSENFQTLPDAGLPQKVAEKLDEIYVAGLVAHSDLDERAIEALKEFNE

Parental  DGALAVLQQFKDSDLSHVQNKSAFLCGVMKTYRQREKQGTKVADSSKGPDEAKIKALLERTGYTLDVTTG
          DGALAVLQQFKDSDLSHVQNKSAFLCGVMKTYRQREKQGTKVADSSKGPDEAKIKALLERTGY.LDVTTG
Retrocopy DGALAVLQQFKDSDLSHVQNKSAFLCGVMKTYRQREKQGTKVADSSKGPDEAKIKALLERTGYILDVTTG

Parental  QRKYGGPPPDSVYSGQQPSVGTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTF
          QRKYGGPPPDSVYSGQQPSVGTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTF
Retrocopy QRKYGGPPPDSVYSGQQPSVGTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTF

Parental  CTKEAAQEAVKLYNNHEIRSGKHIGVCISVANNRLFVGSIPKSKTKEQILEEFSKVTEGLTDVILYHQPD
          CTKEAAQEAVKLYNNHE.RSGKHIGVCISVANNRLFVGSIPKSKTKEQILEEFSKVTEGLTDVILYHQPD
Retrocopy CTKEAAQEAVKLYNNHETRSGKHIGVCISVANNRLFVGSIPKSKTKEQILEEFSKVTEGLTDVILYHQPD

Parental  DK-KKNRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVGTVEWADPIEDPDPEVMAKVKVLFVRNLANTV
          DK....RGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVGTVEWADPIEDPDPEVMAKVKVLFVRNLANTV
Retrocopy DK>XXXRGFCFLEYEDHKTAAQARRRLMSGKVKVWGNVGTVEWADPIEDPDPEVMAKVKVLFVRNLANTV

Parental  TEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQ
          TEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQ
Retrocopy TEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQ

Parental  RQAAKNQM
          RQAAKNQM
Retrocopy RQAAKNQM

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	0.22 RPM	23.75 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	31.10 RPM
SRP007412_cerebellum	0.13 RPM	24.15 RPM
SRP007412_heart	0.12 RPM	30.27 RPM
SRP007412_kidney	0.23 RPM	31.34 RPM
SRP007412_liver	0.08 RPM	17.22 RPM
SRP007412_testis	0.34 RPM	33.96 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1843 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1843 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1843 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000018345	1 retrocopy	retro_dnov_1927,
Homo sapiens	ENSG00000135316	1 retrocopy	retro_hsap_2410,
Macaca mulatta	ENSMMUG00000010970	1 retrocopy	retro_mmul_2433,
Macaca mulatta	ENSMMUG00000012575	1 retrocopy	retro_mmul_1843 ,
Nomascus leucogenys	ENSNLEG00000012879	1 retrocopy	retro_nleu_162,
Oryctolagus cuniculus	ENSOCUG00000000601	1 retrocopy	retro_ocun_1683,
Pongo abelii	ENSPPYG00000016819	1 retrocopy	retro_pabe_1775,
Pan troglodytes	ENSPTRG00000018393	1 retrocopy	retro_ptro_1387,
Rattus norvegicus	ENSRNOG00000000204	1 retrocopy	retro_rnor_805,
Sus scrofa	ENSSSCG00000004294	1 retrocopy	retro_sscr_436,
Vicugna pacos	ENSVPAG00000001061	1 retrocopy	retro_vpac_391,