RetrogeneDB ID: retro_mmus_3007

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:18578348..18579022(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Trmt10a
• Ensembl ID: ENSMUSG00000004127
• Aliases: Trmt10a, 3110023L08Rik, AA794508, Rg9mtd2, Rnmtd2
• Description: tRNA methyltransferase 10A [Source:MGI Symbol;Acc:MGI:1920421]

Sequence

>retro_mmus_3007
TCTGAAATGCTGCCAGCATCCAGTGAGTCTCCTAATGTGGAAAAAAAGCTGGGGGCGAGTGATGGTGAAGAGGAGAGACA
GAAGCTGAGAGTGGATGCAAGGGCTGAGCCAGTATCTAAATGGCAACTGAAGAAGTGGATGAAACAAAAATAGTGGGACA
AGCAAAGGGAACAGGACAAGGAAAAATGAAAAGAAAAACGCAAGAGAAAGGAATTAGAACAACGTCAGCTGGAGTCCAAC
TCAGATGGAAACGACAGAAAGTGTATTGGGAGCGATGTTGCTCGTAGCAGCCTCAGCCTGGTCATCGACTGTAGCTTTGA
TGACTTGATGGTGTTAAAGGATATTAAGAAACTTCATAAACAGATTCAATGATGTTATGCAGAAAACCACCAGGCATCTC
ATCCTGTGCAGTTTTACTTGACAAGCTGTGGAGGTCAATTGAAGAAGAACATGGATGAGAATGACCAATGATGGGCAACT
GGAAGAATATTCACATCAAATCTGAGCACTATAGTGAACTCATAAAAAAAGAAGACCTGGTTTATCTGACATCAGACTCA
CCTAATGTACTGAAGGACTTAGATGAGTCAAAGGCCTACATGATTGGAGGACTAGTGGACCACAACCATCACAAGGAACT
CACATTTAAACAAGCATCCAGTTACTGAATCGAA

Alignment

ORF - retro_mmus_3007 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.96 %
• Parental protein coverage: 68.18 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SEMLPASIESTNVEEKLGTSDGEEERQEPRVDAGAEPISKRQLKKLMKQKQWEEQREQRKEKRKEKRKRK
          SEMLPAS.ES.NVE.KLG.SDGEEERQ..RVDA.AEP.SK.QLKK.MKQK.W..QREQ.KEK.KEKRKRK
Retrocopy SEMLPASSESPNVEKKLGASDGEEERQKLRVDARAEPVSKWQLKKWMKQK*WDKQREQDKEK*KEKRKRK

Parental  KLERRQLESNSDGNDRKRVRRDVARSSLRLVIDCSFDDLMVLKDIKKLHKQIQRCYAENRRASHPVQFYL
          .LE.RQLESNSDGNDRK....DVARSSL.LVIDCSFDDLMVLKDIKKLHKQIQ.CYAEN..ASHPVQFYL
Retrocopy ELEQRQLESNSDGNDRKCIGSDVARSSLSLVIDCSFDDLMVLKDIKKLHKQIQ*CYAENHQASHPVQFYL

Parental  TSHGGQLKKNMDENDQGWV-NWKDIHIKSEHYSELIKKEDLVYLTSDSPNVLKDLDESKAYVIGGLVDHN
          TS.GGQLKKNMDENDQ.W..NWK.IHIKSEHYSELIKKEDLVYLTSDSPNVLKDLDESKAY.IGGLVDHN
Retrocopy TSCGGQLKKNMDENDQ*WA<NWKNIHIKSEHYSELIKKEDLVYLTSDSPNVLKDLDESKAYMIGGLVDHN

Parental  HHKGLTFKQATSYGIE
          HHK.LTFKQA.SY.IE
Retrocopy HHKELTFKQASSY*IE

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	5.89 RPM
SRP007412_cerebellum	0.00 RPM	4.86 RPM
SRP007412_heart	0.00 RPM	1.81 RPM
SRP007412_kidney	0.00 RPM	4.31 RPM
SRP007412_liver	0.00 RPM	4.34 RPM
SRP007412_testis	0.00 RPM	66.64 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3007 was not detected

EST

No EST(s) were mapped for retro_mmus_3007 retrocopy.

TSS

No TSS is located nearby retro_mmus_3007 retrocopy 5' end.

Lab

retro_mmus_3007 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3007 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001076	1 retrocopy	retro_amel_1868,
Macaca mulatta	ENSMMUG00000009090	1 retrocopy	retro_mmul_2024,
Mus musculus	ENSMUSG00000004127	3 retrocopies	retro_mmus_3007 , retro_mmus_3008, retro_mmus_3368,
Oryctolagus cuniculus	ENSOCUG00000015213	1 retrocopy	retro_ocun_1482,
Otolemur garnettii	ENSOGAG00000005330	2 retrocopies	retro_ogar_2061, retro_ogar_3335,
Ictidomys tridecemlineatus	ENSSTOG00000005064	1 retrocopy	retro_itri_1131,