RetrogeneDB ID: retro_itri_22

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393431.1:2259911..2260766(+)
• Located in intron of: ENSSTOG00000006585

Retrocopy information

• Ensembl ID: ENSSTOG00000021075
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000015877
• Aliases: None
• Description: None

Sequence

>retro_itri_22
ATGACCTCGCTGACCCAACGCAGCTCGGGCTTGGTGCAGCGGCGCACTGAGGCCTCCTGTAACGCCGCCCAGAGCCGCCG
CGACGAGCAGGATGACGACGACAAGGGCGACTCCAAGGAAACGCGGCTGACCGTGATGGAGGAGGTGCTCCTGCTGGGCC
TCAAGGACCGAGAGGGTTATACATCATTTTGGAATGACTGTATATCATCTGGATTACGTGGCTGTGTGTTGATTGAATTA
GCATTGAGAGGAAGGTTACAACTAGAGGCTTGTGGAATGAGACGTAAAAGTCTTTTAACAAGAAAGGTGACAAGAAAGGT
GATTTGTAAGTCCGATGCACCAACAGGGGATGTTCTTCTGGATGAAGCTCTAAATCATGTTGAGGAGACTCAACCTCCAG
AAACAGTCCAGAACTGGATTGAATTACTTAGTGGTGAGACATGGAATCCATTAAAATTGCATTATCAATTAAGAAACGTG
AGGGAACGATTAGCTAAAAACCTGGTGGAAAAGGGTGTACTGACGACAGAGAAACAGAACTTCCTACTTTTTGACATGAC
GACACATCCTCTCACCAATAACAACATTAAGCAGCACCTCATCAAGAAGGTACAAGAAGCTGTTCTTGACAAATGGGTGA
ATGACCCTCACCGCATGGACAAGCGCTTGCTGGCTCTCATTTACTTAGCCCATGCCTCGGATGTCCTGGAGAATGCCTTT
GCACCTCTTCTGGATGAGCAGTATGACTTAGCTACCAAGAGAGTGCAGCTTCTTGACTTAGACCCCGAGGTGGAATGTCT
GAAGGCCAACACCAACGAGGTTCTGTGGGCAGTGGTGGCGGCATTCACCAAGTAA

Alignment

ORF - retro_itri_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.58 %
• Parental protein coverage: 86.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSFWNDCISSGLRGCMLIELALRGRLQLEACG
          AQSRRDEQDDDDKGDSKETRLT.MEEVLLLGLKDREGYTSFWNDCISSGLRGC.LIELALRGRLQLEACG
Retrocopy AQSRRDEQDDDDKGDSKETRLTVMEEVLLLGLKDREGYTSFWNDCISSGLRGCVLIELALRGRLQLEACG

Parental  MRRKSLL----TRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGETWNPLKLHYQLRNVRE
          MRRKSLL....TRKVICKSDAPTGDVLLDEAL.HV.ETQPPETVQNWIELLSGETWNPLKLHYQLRNVRE
Retrocopy MRRKSLLTRKVTRKVICKSDAPTGDVLLDEALNHVEETQPPETVQNWIELLSGETWNPLKLHYQLRNVRE

Parental  RLAKNLVEKGVLTTEKQNFLLFDMTTHPLTNNNIKQHLIKKVQEAVLDKWVNDPHRMDKRLLALIYLAHA
          RLAKNLVEKGVLTTEKQNFLLFDMTTHPLTNNNIKQHLIKKVQEAVLDKWVNDPHRMDKRLLALIYLAHA
Retrocopy RLAKNLVEKGVLTTEKQNFLLFDMTTHPLTNNNIKQHLIKKVQEAVLDKWVNDPHRMDKRLLALIYLAHA

Parental  SDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK
          SDVLENAFAPLLDEQYDLATKRV.QLLDLDPEVECLKANTNEVLWAVVAAFTK
Retrocopy SDVLENAFAPLLDEQYDLATKRV-QLLDLDPEVECLKANTNEVLWAVVAAFTK

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_22 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_22 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
Ictidomys tridecemlineatus	ENSSTOG00000015877	1 retrocopy	retro_itri_22 ,
Tupaia belangeri	ENSTBEG00000009923	1 retrocopy	retro_tbel_3352,