RetrogeneDB ID: retro_itri_507

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393297.1:11217355..11217771(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TK2
• Ensembl ID: ENSSTOG00000029024
• Aliases: None
• Description: thymidine kinase 2, mitochondrial [Source:HGNC Symbol;Acc:11831]

Sequence

>retro_itri_507
CCTGTATGACTGATGGAAAAGTCATTTCACAGCACAAGACACATTTTTGTAGAAAACCTGTACAGAAGAGGGAAGGTACC
TGAAGTGGACAATGTGATTCTCTCTGAATGGTTTGACTGGATCCTGAGGAGCACTGATGTGTCCATTGACCTGATAATGT
ATCTCTGTACCACTTCTGAGACCTGTTAGGAGAGATGAAAGACTGAGGTGCAGGCCAGAGGAGGACTGACATTCCACTAC
AGTACCTGGGTGCTCTTCACCAGCTCCATGAGGAGTGGCTCATCACAGGAAGCCTTTTCCCTGTGGCAGCCCCTGTTGTG
GTGACTGAGGCTGACTACAACATGCAGGAAAATTCTGGAACTCTTTGAACAAAACTGACCCCAATATTAACTCCAGAGAA
TTGGAAGCATGGCCCA

Alignment

ORF - retro_itri_507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.94 %
• Parental protein coverage: 54.98 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PVRLMERSLHSARYIFVENLYRSGKMPEVDYVILSEWFDWIVRNIDVSIDLIVYLRTTPETCYERLKK-R
          PV.LME.S.HS.R.IFVENLYR.GK.PEVD.VILSEWFDWI.R..DVSIDLI.YL.TT.ETC.ER.K..R
Retrocopy PV*LMEKSFHSTRHIFVENLYRRGKVPEVDNVILSEWFDWILRSTDVSIDLIMYLCTTSETC*ER*KT>R

Parental  CRQEE-KVIPLEYLSALHQLYEEWLITGSLFPAAAPVLVIEADHNME-KMLELFEQN-RARILTPETWKH
          CR.EE...IPL.YL.ALHQL.EEWLITGSLFP.AAPV.V.EAD.NM..K.LELFEQN....ILTPE.WKH
Retrocopy CRPEE>TDIPLQYLGALHQLHEEWLITGSLFPVAAPVVVTEADYNMQ>KILELFEQN<LTPILTPENWKH

Parental  GP
          GP
Retrocopy GP

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_507 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_507 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000000331	1 retrocopy	retro_meug_812,
Ictidomys tridecemlineatus	ENSSTOG00000029024	1 retrocopy	retro_itri_507 ,