RetrogeneDB ID: retro_mmus_3586

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:23854818..23856034(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081812
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tes
• Ensembl ID: ENSMUSG00000029552
• Aliases: Tes, D6Ertd352e, TESS, Tes1, Tes2, testin2
• Description: testis derived transcript [Source:MGI Symbol;Acc:MGI:105081]

Sequence

>retro_mmus_3586
ATGGATTTAGGTCACAAGCAAAGACTGGGAGCCCCCTCTCTAAAATGCAAAGAAAATATTGCAGGGTTTGAAATACACTT
TTGGAGAAAAATATGTTGTAACTGCAAATATGGGACAGAAGAGCATGACATACTCCTAAGCAATGATGAGGAGCAGAAAG
TAGGGAGACTCTTTGAAGACACCAAGTACACCATGTTGATCAAGCTGAATTCAGATGAAATTCCCAAGTGCAAATGCTGT
GCTATGAAAAGGACTAATCCACGTGCTGCCAAGAAGAAAGTTACTTTCAATACTGTTGTCTATGAGTGGGCTCCTCTTGT
CCAGAATCAGGCACTGGCCAGCCAGTATGTGCAGATGCTGCCTAAGGAGAAGCAGCCAGTGTCAGATTCAGAGGGGGCAC
AGTACTGGAAGAAGCAGCTCCCTGCACATGACCAGGACCCTTCTAAGGTGGAATGAGTTGTCTCCCAAAGAGGTGAAAGA
GATGGAGCAGTTTGTGAAGCAATATAAAAGTGAGGCTCTGGGAGTGGGTGATGTGAAGCTTCTCTCTGAGAGGAATGCTC
AAGGTGACAAGGTGCACAACCCTGATGGAGAGAGAAACACCCCAGAAGCAGTGGTTTCCAAGGACAAGTCTATAGAGTCT
AAGAAGACCCAATATTCCTGTTACTGCTGTAAATACCCCATGAAAGAAGGAGACCCAGCCATCTATGCTCAAAGGGCTGG
CTACAGTAAACTCTGGCACCTGGCTTGTTTTATCTGCAGCACCTGTGGTGAACTCCTAGTAAACATGATTTACTTCTGGA
AGAATGGGAAGCTATACTATGGCAGACATTACTGTGACATTGAGAAGCCCTGCTGTGCTAGTTGTGATGAGTTGATATTC
AGCAAGAAATATACCCAAGCAGAAAACAAGAATTGGCATCTGAAACATTTCTCATGCTTTGACTGTGACAAAATCTTGGC
AGGAAACATATATCTTATGATCAGTGACAAGCCTGTGTGCAAGCCCTGCTACATGAAGAACCATGTTGTGGTGTGTCAAG
GATGCCACAGTATCATTGACCCAGAAGAGCTGAGAGTGATCTACAATAACTTCAGCTGGCATGAGTCCACAACATGCTTC
CTATGTTCATGCTGCAGCAAGTGTCTTTTGGGGCAGAAGTTTATACGTGTAAAGGAGATGGTTTTCTGTTCCATGAAGTG
TAAGAAAATGATGTCC

Alignment

ORF - retro_mmus_3586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGLGHEQGFGAPCLKCKENCEGFELHFWRKICRNCKCGQEEHDVLLSNEEDRKVGRLFEDTKYTTLIAKL
          M.LGH.Q..GAP.LKCKEN..GFE.HFWRKIC.NCK.G.EEHD.LLSN.E..KVGRLFEDTKYT.LI.KL
Retrocopy MDLGHKQRLGAPSLKCKENIAGFEIHFWRKICCNCKYGTEEHDILLSNDEEQKVGRLFEDTKYTMLI-KL

Parental  KSDGIPMYKRNVMILTNPVAAKKNVSINTVTYEWAPPVQNQALARQYMQMLPKEKQPVAGSEGAQYRKKQ
          .SD.IP..K...M..TNP.AAKK.V..NTV.YEWAP.VQNQALA.QY.QMLPKEKQPV..SEGAQY.K..
Retrocopy NSDEIPKCKCCAMKRTNPRAAKKKVTFNTVVYEWAPLVQNQALASQYVQMLPKEKQPVSDSEGAQYWK--

Parental  LAKQLPAHDQDPSKC-HELSPKEVKEMEQFVKKYKSEALGVGDVKFPSEMNAQGDKVHNPAGNRHAPAAV
          ..KQLPAHDQDPSK...ELSPKEVKEMEQFVK.YKSEALGVGDVK..SE.NAQGDKVHNP.G.R..P.AV
Retrocopy --KQLPAHDQDPSKV>NELSPKEVKEMEQFVKQYKSEALGVGDVKLLSERNAQGDKVHNPDGERNTPEAV

Parental  ASKDKSAESKKTQYSCYCCKHTMNEGEPAIYAERAGYDKLWHPACFICSTCGELLVDMIYFWKNGKLYCG
          .SKDKS.ESKKTQYSCYCCK..M.EG.PAIYA.RAGY.KLWH.ACFICSTCGELLV.MIYFWKNGKLY.G
Retrocopy VSKDKSIESKKTQYSCYCCKYPMKEGDPAIYAQRAGYSKLWHLACFICSTCGELLVNMIYFWKNGKLYYG

Parental  RHYCDSEKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDHILAGKIYVMVTDKPVCKPCYVKNHAVV
          RHYCD.EKP.CA.CDELIFS..YTQAEN.NWHLKHF.CFDCD.ILAG.IY.M..DKPVCKPCY.KNH.VV
Retrocopy RHYCDIEKPCCASCDELIFSKKYTQAENKNWHLKHFSCFDCDKILAGNIYLMISDKPVCKPCYMKNHVVV

Parental  CQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKRMMS
          CQGCH..IDPE..RV.YNNFSWH.ST.CFLCSCCSKCL.GQKF..V..MVFCS..CK.MMS
Retrocopy CQGCHSIIDPEELRVIYNNFSWHESTTCFLCSCCSKCLLGQKFIRVKEMVFCSMKCKKMMS

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	2.52 RPM
SRP007412_cerebellum	0.00 RPM	2.00 RPM
SRP007412_heart	0.00 RPM	3.33 RPM
SRP007412_kidney	0.00 RPM	23.45 RPM
SRP007412_liver	0.00 RPM	2.38 RPM
SRP007412_testis	0.00 RPM	87.82 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3586 was not detected

EST

No EST(s) were mapped for retro_mmus_3586 retrocopy.

TSS

No TSS is located nearby retro_mmus_3586 retrocopy 5' end.

Lab

retro_mmus_3586 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3586 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005193	2 retrocopies	retro_cjac_3361, retro_cjac_3870,
Mus musculus	ENSMUSG00000029552	3 retrocopies	retro_mmus_253, retro_mmus_3438, retro_mmus_3586 ,
Rattus norvegicus	ENSRNOG00000032978	3 retrocopies	retro_rnor_2974, retro_rnor_2975, retro_rnor_9,