RetrogeneDB ID: retro_itri_580

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393303.1:1641051..1641345(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL5B
• Ensembl ID: ENSSTOG00000027859
• Aliases: None
• Description: ADP-ribosylation factor-like 5B [Source:HGNC Symbol;Acc:23052]

Sequence

>retro_itri_580
TCTGTAACCAAGTTCATCATTCTCGTTGTTGATAGTATTGACAGGGAACGACTAGCTATTACGAAAGAAGAATTGTACAG
AATGTTGGCTCATGAGGATTTAAGGAAAGCTGCAGTCCTTATCTTTGCAAATAAACAGGATATGAAAGGGTGTATGACGG
CAGATGAAATCTCTAAATACCTCACCCTTAGTTCAATTAAGGATCATCCATGGCACATTCAGTCTTGCTGTGCTTTAACG
GGAGAAGGGTTATGCCAAGGTCTAGAGTGGATGACCTCCCGGATTGGCGTAAAA

Alignment

ORF - retro_itri_580 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.92 %
• Parental protein coverage: 54.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SNTEFIILVVDSIDRERLAITKEELYRMLAHEDLRKAAVLIFANKQDMKGCMTAAEISKYLTLSSIKDHP
          S.T.FIILVVDSIDRERLAITKEELYRMLAHEDLRKAAVLIFANKQDMKGCMTA.EISKYLTLSSIKDHP
Retrocopy SVTKFIILVVDSIDRERLAITKEELYRMLAHEDLRKAAVLIFANKQDMKGCMTADEISKYLTLSSIKDHP

Parental  WHIQSCCALTGEGLCQGLEWMTSRIGVR
          WHIQSCCALTGEGLCQGLEWMTSRIGV.
Retrocopy WHIQSCCALTGEGLCQGLEWMTSRIGVK

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_580 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_580 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005856	2 retrocopies	retro_cpor_558, retro_cpor_747,
Macaca mulatta	ENSMMUG00000007453	3 retrocopies	retro_mmul_614, retro_mmul_726, retro_mmul_743,
Oryctolagus cuniculus	ENSOCUG00000014876	1 retrocopy	retro_ocun_79,
Ictidomys tridecemlineatus	ENSSTOG00000011104	1 retrocopy	retro_itri_1390,
Ictidomys tridecemlineatus	ENSSTOG00000016022	2 retrocopies	retro_itri_1000, retro_itri_348,
Ictidomys tridecemlineatus	ENSSTOG00000016326	1 retrocopy	retro_itri_62,
Ictidomys tridecemlineatus	ENSSTOG00000027859	1 retrocopy	retro_itri_580 ,