RetrogeneDB ID: retro_itri_317

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393284.1:5427945..5428494(+)
• Located in intron of: ENSSTOG00000014899

Retrocopy information

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

Parental gene information

• Parental gene symbol: AHSA1
• Ensembl ID: ENSSTOG00000003196
• Aliases: None
• Description: AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast) [Source:HGNC Symbol;Acc:1189]

Sequence

>retro_itri_317
AAAACAGAGTTCACCCAGGGCATGATCTTGCAGACAGTGAATGGAGAGTGAGTAGACCCAACAGGGGAGCCAGCACTGAA
AACTGAGGCACACAAGACTAACTCTGCTCCTCAAACAAACCCAGGCCAAACCTGGTGGTGTCAAAATGCCCCGTTTATAA
GAGCAACCTTAGAGAGACCTTCTCCGACATCCCCAGAGGAACTCTATAGAGAGTTAACCACCCAAGGCTGGTTCAGGCCT
TTACCCATGATCCCACAATGTCAGAAGCAGACAAAGGTGAGAAGTTTCACATGGAGATGGCAGTGTCTCTGGGGAATTTT
CTGATCCAGTTCCTGAAAAACATACTGCGATGAAGGGAGGTTTAACTCTTGGCCAAAGGGGCACTTTGCTACCATCATGT
TGACCTTCATTGACAAGAGTGGAGAGACTGAGCTGTGCATGGAAGGCCGAGGCATCCTTGACCCTGAGGAGGAGAGGACA
CAGCAGGGCTGGCAGCGGTACTACACTGAAGGCATTGAACAGACCTCTGGCTATGGAGCACATTGTTTT

Alignment

ORF - retro_itri_317 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.13 %
• Parental protein coverage: 54.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KTEFTQGMILPTVNGESVDPTAQPAPKTEERKTKSAPQ-KTQAKPVGVKIPTC-KITLRETFL-TSPEEL
          KTEFTQGMIL.TVNGE.VDPT..PA.KTE..KT.SAPQ..TQAKP.GVK.P...K..LRETF..TSPEEL
Retrocopy KTEFTQGMILQTVNGE*VDPTGEPALKTEAHKTNSAPQ>QTQAKPGGVKMPRL>KSNLRETFS>TSPEEL

Parental  YRVFTTQ-ELVQAFTHAPAMLEADKGGKFHMV-DGNVSGEFTDLVPEKHIAMKW-RFKSWPEGHFATITL
          YR..TTQ..LVQAFTH.P.M.EADKG.KFHM..DG.VSGEF.D.VPEKH.AMK..RF.SWP.GHFATI.L
Retrocopy YRELTTQ<RLVQAFTHDPTMSEADKGEKFHME<DGSVSGEFSDPVPEKHTAMKG<RFNSWPKGHFATIML

Parental  TFTDKSGETELCMEGRGIPAPEEERTRQGWQRYYFEGIKQTFGYGARLF
          TF.DKSGETELCMEGRGI..PEEERT.QGWQRYY.EGI.QT.GYGA..F
Retrocopy TFIDKSGETELCMEGRGILDPEEERTQQGWQRYYTEGIEQTSGYGAHCF

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_317 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_317 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
Dipodomys ordii	ENSDORG00000012969	1 retrocopy	retro_dord_687,
Ictidomys tridecemlineatus	ENSSTOG00000003196	1 retrocopy	retro_itri_317 ,