RetrogeneDB ID: retro_itri_1131

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393383.1:3378687..3379190(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRMT10A
• Ensembl ID: ENSSTOG00000005064
• Aliases: None
• Description: tRNA methyltransferase 10 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:28403]

Sequence

>retro_itri_1131
AGATATTATGCAGATAACCAACAAGCACTGCATCCTGTGCAGTTTTACTTCACCAGCTGAGGAGGTGGACTGGAGAAGAA
CCTGGATGAAAATGGCAAAGGATGCATCGTCTGGAAGGATATCCACGTCAACCTGGAACACTATAATGAACTCATAAGAA
AAGAAGATCTGATTTATCTTACATCAGCTTTGCTAGTATGATAAAGGAATGAGATGAATCAAAGGCATATGTGATTGGTG
GATTAGTAGATCACAACCATCACAAGAGATTCACATATAAACAAGCATCAGATTAGGGAACTGATCGTGTACCACTCCCC
CTGGAAATTTTGTGAAAATTTATAATTGAAAGTTTTGGCAGTTAAAAAAAATGTATTTGAAATTGTTCTGGAAGATCCCA
GAAACAAGAGACTGGCAAGAAGCCTTTTTTCACTATCTTACTCTAAAGGAAAGGGGGTGTTCTCATAGACAAAGCTCGTG
AAAGTTCTTCCCATGACAAGCAG

Alignment

ORF - retro_itri_1131 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.12 %
• Parental protein coverage: 59.64 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RCYAENRRALHPVQFYLTSHGGQLKKNMDENDKGWVNWKDIHIKPEHYSELIKKEDLIYLTS-DSPNILK
          R.YA.N..ALHPVQFY.TS.GG.L.KN.DEN.KG...WKDIH...EHY.ELI.KEDLIYLTS.......K
Retrocopy RYYADNQQALHPVQFYFTS*GGGLEKNLDENGKGCIVWKDIHVNLEHYNELIRKEDLIYLTS<SFASMIK

Parental  ELDESKAYVIGGLVDHNHHKGFTYKQASDFGIHHAQLPL-GSFVKMNS-RKVLAV-NHVFEIILGYLETR
          E.DESKAYVIGGLVDHNHHK.FTYKQASD.G.....LPL.G.FVK.....KVLAV...VFEI.L......
Retrocopy E*DESKAYVIGGLVDHNHHKRFTYKQASD*GTDRVPLPL<GNFVKIYN<LKVLAVXXXVFEIVLEDPRNK

Parental  NWQEAFFTI-LPQRKG-AVPTDKACESSSQDKQ
          ......F.......KG..V..DKA.ESSS.DKQ
Retrocopy RLARSLFSLSYSKGKG<GVLIDKARESSSHDKQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1131 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1131 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
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 ,