RetrogeneDB ID: retro_itri_1338

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393446.1:138538..138966(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2G2
• Ensembl ID: ENSSTOG00000007968
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2G 2 [Source:HGNC Symbol;Acc:12483]

Sequence

>retro_itri_1338
TCAGGCCCCATGAATGAAGAGAATTTTTTTTTTTTTGAAAGGGAGGTATTGATCATGGGCCCTGAAGATACCTGTTTTTG
AGTTTGGTGTTTTTCCTGCTACCTTGAGTTTGTTTCCCACCTGACTACCACTGAATCTTCCCAAGATGAGGTTCACTTGC
GAGATGTTCCATCCCAGCATCTACCGGGACTGGCAGAGTTTGCATCTCCATCCTCCACAAACCGGGTGATGACCCCATAG
GCTTCAAGAGAGGCTCTGAGATGGGGAGCCCCTGGCTGAGTGTGGAAAAGATCCTGCTGTGAGTGACGGGCATTCTGGCG
GAGCCCAGTGATGAAAGTGGAGCTAATGTGGATGCTTCCAAAATGTGAGGTGACTGGAAGCAGTTTTACAAGACTGCCAG
TCAGATCTTGCAGAAGTCTCTGGGACTC

Alignment

ORF - retro_itri_1338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.66 %
• Parental protein coverage: 84.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGPMNEENFF--EWEALIMGPEDTCF-EFGVFPAILS-FPLDYPLSPPKMRFTCEMFHPNIYPD-GRVCI
          .GPMNEE.....E.E.LIMGPEDTCF.EFGVFPA.LS.FP...PL..PKMRFTCEMFHP.IY.D.GRVCI
Retrocopy SGPMNEEXXXXXEREVLIMGPEDTCF>EFGVFPATLSLFPT*LPLNLPKMRFTCEMFHPSIYRD>GRVCI

Parental  SILHAPGDDPMGYESSAERWSPVQSVEKILLSVVSMLAEPNDESGANVDASKMWRDDREQFYRIARQIVQ
          SILH.PGDDP.G.....E..SP..SVEKILL.V...LAEP.DESGANVDASKM...D..QFY..A.QI.Q
Retrocopy SILHKPGDDPIGFKRGSEMGSPWLSVEKILL*VTGILAEPSDESGANVDASKM-*GDWKQFYKTASQILQ

Parental  KSLGL
          KSLGL
Retrocopy KSLGL

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_1338 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1338 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000001963	1 retrocopy	retro_lafr_1049,
Ictidomys tridecemlineatus	ENSSTOG00000007968	1 retrocopy	retro_itri_1338 ,
Ictidomys tridecemlineatus	ENSSTOG00000023255	1 retrocopy	retro_itri_822,