RetrogeneDB ID: retro_itri_958

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393349.1:1540310..1540710(-)
• Located in intron of: ENSSTOG00000006263

Retrocopy information

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

Parental gene information

• Parental gene symbol: NKIRAS2
• Ensembl ID: ENSSTOG00000006159
• Aliases: None
• Description: NFKB inhibitor interacting Ras-like 2 [Source:HGNC Symbol;Acc:17898]

Sequence

>retro_itri_958
AAGAGCTGCAAGAGATGCATGTGTGGTCAGGCATCTGTGGGTAAAATTTCAATCCTAGAACAGCTCCTGTATGGGAATCA
TGTAGTGGGTTCTGAGATGACTGAAATCCAGGAAGACACTTACGTAGGTTCTACTGAGATAGACCGGGAAGTGCGGGAGC
AGGTGCATTCCTATAATACCTAGGGGGCTTCAAAATGGGGCCAAGCTGCCACAGCCCTGCTTCTCCTGCACTAATGGCCA
CATCCTGGTCTACAGCACAGATGGCTGAGAGTCCTTTCAGCATGTGGAGCTACTCAAGAAGGAGACTGACAAATCTAAGG
ATAAGACGGAGATCACCACTGTGGTCCTGGGCAACATGTGTGACTTACAGGAACAGCGGCGTGTAGACCCAGATATGGCT

Alignment

ORF - retro_itri_958 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.87 %
• Parental protein coverage: 69.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KSCKVVVCGQASVGKTSILEQLLYGNHVVGSEMIETQEDIYVGSIETDRGVREQVRFYDT-RGLRDGAEL
          KSCK...CGQASVGK.SILEQLLYGNHVVGSEM.E.QED.YVGS.E.DR.VREQV..Y.T.RGL..GA.L
Retrocopy KSCKRCMCGQASVGKISILEQLLYGNHVVGSEMTEIQEDTYVGSTEIDREVREQVHSYNT>RGLQNGAKL

Parental  PRHCFSCTDGYVLVYSTDSRESFQRVELLKKEIDKSKDKKEVTIVVLGNKCDLQEQRRVDPDVA
          P..CFSCT.G..LVYSTD..ESFQ.VELLKKE.DKSKDK.E.T.VVLGN.CDLQEQRRVDPD.A
Retrocopy PQPCFSCTNGHILVYSTDG*ESFQHVELLKKETDKSKDKTEITTVVLGNMCDLQEQRRVDPDMA

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_958 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_958 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	ENSSTOG00000006159	1 retrocopy	retro_itri_958 ,
Tursiops truncatus	ENSTTRG00000006623	1 retrocopy	retro_ttru_453,