RetrogeneDB ID: retro_itri_55

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393288.1:15229200..15229980(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000022710
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000008527
• Aliases: None
• Description: None

Sequence

>retro_itri_55
ATGGCAGTTCGCCGTGCATTAAAAGCTGTTTTGGTAGACCTCAATGGCACACTTCACATTGAAGATGCAGCTGTGCCAGG
CGCACAGGAAGCTCTTAAAAGGTTACGCAGTTCTTCTGTAATTGTTAGGTTTGTGACCAATACAACCAAAGAAAGCAAGC
AAGATCTTTTGGAAAGGTTGAAAAAACTGGAGTTTGATATTTCTGAAGATGAAATATTCACGTCTCTGACTGCAGCCAGA
AGTCTAGTAGAGCAGAAGCAAGTCAGGCCCATGCTGCTGGTTGATGATCGGGCATTACCTGATTTCAAAGGAATACAAAC
AAATGATCCTAATGCTGTGGTCATAGGACTGGCACCAGAACATTTTCATTATCAAACTCTGAACCAAGCATTCCGGTTAC
TCCTGGATGGAGCGCCTCTGATAGCGATCCACAAAGCCAGGTATTACAAGAGAAAAGATGGCTTAGCCCTGGGGCCTGGA
CCCTTTGTGACTGCTTTAGAGTATGCCACTGACACCAGCGCCATAGTAGTGGGGAAACCAGAAAAGACGTTCTTTTTGGA
AGCATTGCGGGGCACTGGCTGTGAACCTGAAGAGGCTGTCATGATAGGAGATGATTGCAGGGATGATGTTGGCGGGGCTC
AAAATGCTGGCATGCTGGGCATTTTAGTAAAAACTGGGAAATACCGAGCAGCAGATGAAGAAAAAATTAGTCCACCTCCC
TACCTAACTTGTGAGAGTTTCTCTCATGCCGTGGACCACATTCTGCAGCATCTCCTGTGA

Alignment

ORF - retro_itri_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.61 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVRRALKAVLVDLNGTLHIEDAAVPGAQEALKRLRSSSVIVRFVTNTTKESKQDLLERLKKLEFDISED
          MAVRRALKAVLVDLNGTLHIEDAAVPGAQEALKRLRSSSVIVRFVTNTTKESKQDLLERLKKLEFDISED
Retrocopy MAVRRALKAVLVDLNGTLHIEDAAVPGAQEALKRLRSSSVIVRFVTNTTKESKQDLLERLKKLEFDISED

Parental  EIFTSLTAARSLVEQKQVRPMLLVDDRALPDFKGIQTNDPNAVVIGLAPEHFHYQTLNQAFRLLLDGAPL
          EIFTSLTAARSLVEQKQVRPMLLVDDRALPDFKGIQTNDPNAVVIGLAPEHFHYQTLNQAFRLLLDGAPL
Retrocopy EIFTSLTAARSLVEQKQVRPMLLVDDRALPDFKGIQTNDPNAVVIGLAPEHFHYQTLNQAFRLLLDGAPL

Parental  IAIHKARYYKRKDGLALGPGPFVTALEYATDTSAIVVGKPEKTFFLEALRGTGCEPEEAVMIGDDCRDDV
          IAIHKARYYKRKDGLALGPGPFVTALEYATDTSAIVVGKPEKTFFLEALRGTGCEPEEAVMIGDDCRDDV
Retrocopy IAIHKARYYKRKDGLALGPGPFVTALEYATDTSAIVVGKPEKTFFLEALRGTGCEPEEAVMIGDDCRDDV

Parental  GGAQNAGMLGILVKTGKYRAADEEKISPPPYLTCESFPHAVDHILQHLL
          GGAQNAGMLGILVKTGKYRAADEEKISPPPYLTCESF.HAVDHILQHLL
Retrocopy GGAQNAGMLGILVKTGKYRAADEEKISPPPYLTCESFSHAVDHILQHLL

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_55 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_55 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011893	1 retrocopy	retro_btau_1336,
Choloepus hoffmanni	ENSCHOG00000009397	1 retrocopy	retro_chof_100,
Macaca mulatta	ENSMMUG00000010999	1 retrocopy	retro_mmul_595,
Ictidomys tridecemlineatus	ENSSTOG00000008527	1 retrocopy	retro_itri_55 ,