RetrogeneDB ID: retro_mmul_1664

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:10449559..10450134(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000010340
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS9
• Ensembl ID: ENSMMUG00000022552
• Aliases: None
• Description: 40S ribosomal protein S9 [Source:RefSeq peptide;Acc:NP_001252588]

Sequence

>retro_mmul_1664
CCAGCGGCCCGGAGCTGGGTTTGTCGCAAAACTTATGTGACCCCGCAGAGACCCTTCGAGAAATCTCATCTCGACCAAAA
GCTGAAGCTGATTGGCGAGTATGGGCTCCAGAACAAATGTGAGGTGTGGAGGGTCAAATTTACCCTGGTCAAGATCCACA
AGGCTGCCAGGGAGCCGCTGACACTTGACGAGAAGGACCCACAGCTTCTGTTCGAAGTCACTCCCTGCTGCAGTGGCTGG
TCCGCACTGGGGAGCTGGATGAGGGAAAGATGAAGCTGGATTACATCGTGGGCCTGAAGATCGATGATTTCTTAGAGAGA
TGCCTACAGACCCAGGTCTTCAAGCTGGGCTTGGGTAAGTCCATCCGCCACGGTTGTGTGCTTATCCGCCAGGTCATATC
CGTGTCCATGAGCAGGTGGTGAATATCCCGTTTTTCACTGTCCGCCTGGATTCCCAGAAGCAATCGACTTCTCCCTCTGC
CTCCCTATGGGGGTGGCCACCCCAGCCACGTGAAGAGGAAGAATGCCAAGATGGACCAGGGTGGGGCTGGAGCCAGAGAT
GACAAGGAGGAGGAT

Alignment

ORF - retro_mmul_1664 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.66 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRRL
          P.ARSWVCRKTYVTP.RPFEKS.LDQ.LKLIGEYGL.NK.EVWRVKFTL.KI.KAARE.LTLDEKDP..L
Retrocopy PAARSWVCRKTYVTPQRPFEKSHLDQKLKLIGEYGLQNKCEVWRVKFTLVKIHKAAREPLTLDEKDPQLL

Parental  FE-GNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQ-RHIRVRK
          FE....LL..LVR.G.LDEGKMKLDYI.GLKI.DFLER.LQTQVFKLGL.KSI.H..VLIRQ..HIRV..
Retrocopy FE<SHSLLQWLVRTGELDEGKMKLDYIVGLKIDDFLERCLQTQVFKLGLGKSIRHGCVLIRQ<GHIRVHE

Parental  QVVNIPSFIVRLDSQKH-IDFSL-RSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED
          QVVNIP.F.VRLDSQK..IDFSL...PYGGG.P..VKRKNAK..QGGAGA.DD.EED
Retrocopy QVVNIPFFTVRLDSQKQ<IDFSL<LPPYGGGHPSHVKRKNAKMDQGGAGARDDKEED

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	0.78 RPM	35.74 RPM
SRP007412_brain_prefrontal_cortex	0.63 RPM	90.20 RPM
SRP007412_cerebellum	0.32 RPM	31.58 RPM
SRP007412_heart	0.12 RPM	121.72 RPM
SRP007412_kidney	0.47 RPM	104.93 RPM
SRP007412_liver	0.00 RPM	129.87 RPM
SRP007412_testis	0.04 RPM	79.68 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1664 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1664 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1664 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_32
Pongo abelii	retro_pabe_1845

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000022552	2 retrocopies	retro_mmul_1664 , retro_mmul_2027,
Mustela putorius furo	ENSMPUG00000010394	1 retrocopy	retro_mputfur_128,
Nomascus leucogenys	ENSNLEG00000006314	1 retrocopy	retro_nleu_91,
Pongo abelii	ENSPPYG00000010377	5 retrocopies	retro_pabe_1343, retro_pabe_1701, retro_pabe_1845, retro_pabe_1887, retro_pabe_2671,
Rattus norvegicus	ENSRNOG00000011355	7 retrocopies	retro_rnor_1298, retro_rnor_2577, retro_rnor_2849, retro_rnor_2902, retro_rnor_635, retro_rnor_663, retro_rnor_892,
Rattus norvegicus	ENSRNOG00000049813	3 retrocopies	retro_rnor_2082, retro_rnor_30, retro_rnor_78,