RetrogeneDB ID: retro_mmus_3082

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:120064476..120065026(-)
• Located in intron of: ENSMUSG00000052273

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rps9
• Ensembl ID: ENSMUSG00000006333
• Aliases: Rps9, 3010033P07Rik, AL022771, AL022885
• Description: ribosomal protein S9 [Source:MGI Symbol;Acc:MGI:1924096]

Sequence

>retro_mmus_3082
AGATGCTTGTTTTGCCATAAAACCTTTGTGACCCCACAGAGACTCTTTGAGAAATTGCATCCCATTCAGAAACTAAAGCT
GATTGGCAAACATAGGCTATGCAACAAACATGAGGTCTGGAGGGTCAAATTTACCTTGGCCAAGACTCACAAGGCCTTCC
AGAAGCTGATGATACTGGACTAATAGGACCCAGGGCATCTTCCTGAGGTCAATGTCCTTCTGCAGTGATCCATAAGCATT
GGGGTGCTGAACGGGGAAACTGAATTATATGTAGGCCTGAAGATGGAGGATTTCTTGGAGAATCAGCTTCAGGCCCAGGT
CTGTAAAATGTACCTGGACAAGGCTATCCACTACACCTGCGTGCTCATCTACCAGCACCATATCAGAGTCAGTAAGAGGT
GATGCACATCCCACCCTTCATTATCTGTCTGGCCTGCCAGAAGCATGCTGACACCTCCCTTTGCCCTCCTAATAGTGGCC
ACCTAGGCCATGTGAAGAATGCCAAGAAGGACCAATGTGGCGCAAGAGCTGTGATGATGAAGCAGAGGAG

Alignment

ORF - retro_mmus_3082 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.17 %
• Parental protein coverage: 97.94 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRRLFEG
          R...C.KT.VTP.R.FEK....Q.LKLIG...L.NK.EVWRVKFTLAK..KA...L..LD..DP..L.E.
Retrocopy RCLFCHKTFVTPQRLFEKLHPIQKLKLIGKHRLCNKHEVWRVKFTLAKTHKAFQKLMILD**DPGHLPEV

Parental  NALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRK-QVVN
          N.LL.....IGVL..G...L....GLK.EDFLE..LQ.QV.K..L.K.IH...VLI.Q.HIRV.K..V..
Retrocopy NVLLQ*SISIGVLN-GETEL--YVGLKMEDFLENQLQAQVCKMYLDKAIHYTCVLIYQHHIRVSK<EVMH

Parental  IPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGA-GDDEEED
          IP.FI..L..QKH.D.SL..P...G..G.V..KNAKK.Q.GA.A..DDE.E.
Retrocopy IPPFIICLACQKHADTSL-CPPNSGHLGHV--KNAKKDQCGARA<CDDEAEE

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	67.85 RPM
SRP007412_cerebellum	0.00 RPM	67.52 RPM
SRP007412_heart	0.00 RPM	154.03 RPM
SRP007412_kidney	0.00 RPM	120.71 RPM
SRP007412_liver	0.00 RPM	120.79 RPM
SRP007412_testis	0.05 RPM	68.47 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3082 was not detected

EST

No EST(s) were mapped for retro_mmus_3082 retrocopy.

TSS

No TSS is located nearby retro_mmus_3082 retrocopy 5' end.

Lab

retro_mmus_3082 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3082 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000027839	4 retrocopies	retro_ggor_1491, retro_ggor_160, retro_ggor_2190, retro_ggor_32,
Mustela putorius furo	ENSMPUG00000010394	1 retrocopy	retro_mputfur_128,
Mus musculus	ENSMUSG00000006333	2 retrocopies	retro_mmus_3082 , retro_mmus_526,
Nomascus leucogenys	ENSNLEG00000006314	1 retrocopy	retro_nleu_91,
Pan troglodytes	ENSPTRG00000011449	1 retrocopy	retro_ptro_57,
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,