RetrogeneDB ID: retro_itri_739

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393315.1:4965274..4965608(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000020010
• Aliases: None
• Description: None

Sequence

>retro_itri_739
ATATTTTCTATGTGTGAACATCATCTGGTTCCATTGGATGGAAATATCCCTGCCTGTTATTTTCCTACCAAGTAAATCCT
TGGCCTCAGCAAGCTTGGAAGGGTGGTAGATATCTATAGTAGGAGAGTGCAAGTTCAAGAGCACCTCATGAAATAAAATT
GCTGTGGCAATCACAGAAGCCTTACAACCTGCTAAAGTCAGAGTAGTGGTAGAAGCAACACACCTTTATGGTATTTCAAA
GGGTGCCAAAAATAAACAGCATAACTGTGACCAGTGTCACATCTTCAGGAAGACCCAAAGATGTGGGGAGAGTTTTTTGA
GTTTCATTCAGAGC

Alignment

ORF - retro_itri_739 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.91 %
• Parental protein coverage: 76.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFSMCEHHLVPFVGKVHIGYLPNKQVLGLSKLARIVEIYSRRLQVQERLTK-QIAVAITEALQPAGVGVV
          .FSMCEHHLVP..G.....Y.P.K..LGLSKL.R.V.IYSRR.QVQE.L.K..IAVAITEALQPA.V.VV
Retrocopy IFSMCEHHLVPLDGNIPACYFPTK*ILGLSKLGRVVDIYSRRVQVQEHLMK>KIAVAITEALQPAKVRVV

Parental  VEATHMCMVMRGVQKMNSKTVTSTMLGVFREDPKTREEFLTLIRS
          VEATH......G......K.........FR......E.FL..I.S
Retrocopy VEATHLYGISKGAK---NKQHNCDQCHIFRKTQRCGESFLSFIQS

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_739 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_739 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000003060	1 retrocopy	retro_ocun_1206,
Ictidomys tridecemlineatus	ENSSTOG00000020010	2 retrocopies	retro_itri_739 , retro_itri_92,