RetrogeneDB ID: retro_itri_997

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393357.1:1974189..1974584(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000025778
• Aliases: None
• Description: None

Sequence

>retro_itri_997
TTCCCATGGTGGTAACAATTAACATCAAAAGTCATCTTTTTCTGGCTTTTTGTCCTTTATCTTCTTCAAGTTGCTGTACT
AGTATTATTCTGTCCACTTCCAGCCCACATGGTATACCTCTGACAGAAGTGATCTGGCAGACATGGCTGATGCTGCTCTT
GGGAACTCTGAATTGCCATATTGTTTCAACAAGAATATCCAAACCCATTAGGTACAGGCAATAAAAGAGAGGTAAATTAA
GAAAAGCAGCTCATTTGGACAGACATAGGGAAGAAGATGGTTCTAGTATCACAGCAAACACACAGGAAGGAGCATTTCAG
AGCCACAGTACAAGCACCACTTACCGTGTTGATACTGTCTTCAGAGATCTCTGGAATGGTGCTTTCTTTTTATCA

Alignment

ORF - retro_itri_997 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.81 %
• Parental protein coverage: 60.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FRWWLQVTSKVIFFWLLVLYLLQVAAIVLFC-STSSPHSIPLTEVIGPIWLMLLLGTVHCQIVSTRT-PK
          F.WW.Q.TSKVIFFWL.VLYLLQVA..VLFC.STSSPH.IPLTEVI...WLMLLLGT..C.IVSTR..P.
Retrocopy FPWW*QLTSKVIFFWLFVLYLLQVAVLVLFC<STSSPHGIPLTEVIWQTWLMLLLGTLNCHIVSTRI>PN

Parental  PISTGGKR-RRKLRKAAHLEVHREGDGSSTTDNTQEGAVQSHGTSTTYSVGAVFRDLWHAAFFLS
          P..TG.KR.R.KLRKAAHL..HRE.DGSS.T.NTQEGA.QSH.TSTTY.V..VFRDLW..AFFLS
Retrocopy PLGTGNKR<RGKLRKAAHLDRHREEDGSSITANTQEGAFQSHSTSTTYRVDTVFRDLWNGAFFLS

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_997 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_997 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000025778	1 retrocopy	retro_itri_997 ,