RetrogeneDB ID: retro_mmus_3438

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:35801193..35802423(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000085107
• 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_3438
GAGATGGACTCAGGTCAAGAGGAAAAATCTGGAGGCCCCTGTCGAAAATGCAAAGAGAAATGCTCAGGTTTTGAACTACA
CTTCTGGAAGAAAATATGTCGTAACTGTAAATGTGGGCCAGAAGAGCATGACATACCCCTGAACACCGAGGAGCACCCGA
AAGTGGGGAAACTCTCTGAGGACATCAAGTACATCAACCTGATCGCCAAGCTGAAGTCAGAGGGAATTCCCATAAACAAC
CGCAATCCTAGGAAATTGTCCAACACAGATGCTTCCAAGAAGAAAGTCTCCACCTACACTCTTATCCATGAGTGTCCTCC
CCCCTTCCGGAACCAGGCATTGCCCAGGAAGTACATGCAGATGCAGCCTAAGGAAAAACAGCCAGTATCAGGTTCAGAGG
GGGCACAGTACCGGAAGAAGCAGCTGGCGAAGCAACTCCCTCCACATGACCAGGACCCTTCTAAGTGCCATGAGTTGTCT
CCCAAAGAGGTAAAGGAGATGGAGCAGTTTGTGAAGAAATACAAATGTGAGGCTCTGGGAGTAGGCGACATGAAGCTTCC
CTGTGAAATTAATGCTCAGTGTTACAAGGAGCACAACCCTGAGGGAGTCAAAAACACCCCAGTAGCAGTGGGTTCCAAGG
GCAAGTCTATGGGGTATAAGAAGACCCAATATTCCTGTTACTGCTGCAAACGCATCATAAAGGAAGGATACCCAGCCATC
TTTGCTGAAAGGGCAGGTTATGATAAACTCTGGCACCCAGGTTGTTTTATCTGCAGCACCTGTGGTGAACTCCTAGTAAA
CATGATTTACTTCTGGAAGAATGGGAAGCTATACTGTGGCAGACATTACTGTGACAGTGAGAAGCCCCGCTGTGCTGGTT
GTGATGAGTTGATATTCAGCAAGGAATACACCCAAGCTGAAAACAAGAATTGGCATCTGAAACACTTCTGCTGTGTTGAC
TGCAAGTACATCCTGGCAGGAAAATTATATGTTATGGTCAATGATAAACCTGTGTGCAAGCCCTGCTACATGAAGAACCA
TGCTGTGGTGTGTCAAGGATGCCACAATGCCATCGACCCAGAAGAGCAGAGAGTAACATACAGTAACTTCAGCTGGCATG
CATCCACAGTGTGCTTCCTATGCTCATACTGCAAGAAGTGTCTTTTTGGGGAGAAATTCATGCCTGTAAATGGGATGATA
TTCTGTTGCAAGGAGTGTAAGAGAATGATG

Alignment

ORF - retro_mmus_3438 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.59 %
• Parental protein coverage: 97.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KMGLGHEQGFGAPCLKCKENCEGFELHFWRKICRNCKCGQEEHDVLLSNEEDRKVGRLFEDTKYTTLIAK
          .M..G.E...G.PC.KCKE.C.GFELHFW.KICRNCKCG.EEHD..L..EE..KVG.L.ED.KY..LIAK
Retrocopy EMDSGQEEKSGGPCRKCKEKCSGFELHFWKKICRNCKCGPEEHDIPLNTEEHPKVGKLSEDIKYINLIAK

Parental  LKSDGIPMYKRNVMILTNPVAAKKNVSINTVTYEWAPPVQNQALARQYMQMLPKEKQPVAGSEGAQYRKK
          LKS.GIP...RN...L.N..A.KK.VS..T...E..PP..NQAL.R.YMQM.PKEKQPV.GSEGAQYRKK
Retrocopy LKSEGIPINNRNPRKLSNTDASKKKVSTYTLIHECPPPFRNQALPRKYMQMQPKEKQPVSGSEGAQYRKK

Parental  QLAKQLPAHDQDPSKCHELSPKEVKEMEQFVKKYKSEALGVGDVKFPSEMNAQGDKVHNPAGNRHAPAAV
          QLAKQLP.HDQDPSKCHELSPKEVKEMEQFVKKYK.EALGVGD.K.P.E.NAQ..K.HNP.G....P.AV
Retrocopy QLAKQLPPHDQDPSKCHELSPKEVKEMEQFVKKYKCEALGVGDMKLPCEINAQCYKEHNPEGVKNTPVAV

Parental  ASKDKSAESKKTQYSCYCCKHTMNEGEPAIYAERAGYDKLWHPACFICSTCGELLVDMIYFWKNGKLYCG
          .SK.KS...KKTQYSCYCCK....EG.PAI.AERAGYDKLWHP.CFICSTCGELLV.MIYFWKNGKLYCG
Retrocopy GSKGKSMGYKKTQYSCYCCKRIIKEGYPAIFAERAGYDKLWHPGCFICSTCGELLVNMIYFWKNGKLYCG

Parental  RHYCDSEKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDHILAGKIYVMVTDKPVCKPCYVKNHAVV
          RHYCDSEKPRCAGCDELIFS.EYTQAEN.NWHLKHFCC.DC..ILAGK.YVMV.DKPVCKPCY.KNHAVV
Retrocopy RHYCDSEKPRCAGCDELIFSKEYTQAENKNWHLKHFCCVDCKYILAGKLYVMVNDKPVCKPCYMKNHAVV

Parental  CQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKRMM
          CQGCHNAIDPE.QRVTY.NFSWHAST.CFLCS.C.KCL.G.KFMPV.GM.FC..ECKRMM
Retrocopy CQGCHNAIDPEEQRVTYSNFSWHASTVCFLCSYCKKCLFGEKFMPVNGMIFCCKECKRMM

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	0.03 RPM	2.38 RPM
SRP007412_testis	6.54 RPM	87.82 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3438 was not detected

EST

No EST(s) were mapped for retro_mmus_3438 retrocopy.

TSS

No TSS is located nearby retro_mmus_3438 retrocopy 5' end.

Lab

retro_mmus_3438 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3438 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,