RetrogeneDB ID: retro_itri_219

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393280.1:33437987..33438403(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IAH1
• Ensembl ID: ENSSTOG00000004500
• Aliases: None
• Description: isoamyl acetate-hydrolyzing esterase 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:27696]

Sequence

>retro_itri_219
CAGTTTTCTTTTCAGCAGGGTGGATGGGGAGCATCATTAGCTGACAAACTGGTAAGAAAACGTGATGTTCTGAATTGTGG
GTTTTCAGGTTACAATACCAGATGGGCCAAAATTATTCTTCCAAGACTAATCAGGAAAGGGAACAAATTGGACAACCCAG
TAACAGTTACAATTTTCTTTGGCACCAATGACAGTGCACTAAAAGATAAGAATCCCAGGAGCACATTCCCCTGGCAGAGT
ATGTTTCAAACTTAAAAAGCATGATTCAGTACCTGAAGTCAGTGGATGTCCCTGAGCACCGAGTCATACTCATTACACCA
CCTCCACTTTGTGAAACAGCCTGGGAAAAGGAATGCCTCATGCAAGGTTGCAAATTAAATTGCTTGAACTCCATTGTTGG
TGAATATGCCAGTGTG

Alignment

ORF - retro_itri_219 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.14 %
• Parental protein coverage: 62.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QFSFQQGGWGASLADKLVRRCDVLNRGFSGYNTRWAKIILPRLIRKGNNLDNPVVVTIFFGANDSALKDE
          QFSFQQGGWGASLADKLVR..DVLN.GFSGYNTRWAKIILPRLIRKGN.LDNPV.VTIFFG.NDSALKD.
Retrocopy QFSFQQGGWGASLADKLVRKRDVLNCGFSGYNTRWAKIILPRLIRKGNKLDNPVTVTIFFGTNDSALKDK

Parental  NPK-QHIPLEEYVANLKSMVQYLKSVDVPEHRVILITPPPLCETAWEKECIMQGWKINRLNSVVGEYASV
          NP...HIPL.EYV.NLKSM.QYLKSVDVPEHRVILITPPPLCETAWEKEC.MQG.K.N.LNS.VGEYASV
Retrocopy NPR<EHIPLAEYVSNLKSMIQYLKSVDVPEHRVILITPPPLCETAWEKECLMQGCKLNCLNSIVGEYASV

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_219 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_219 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000003840	1 retrocopy	retro_eeur_158,
Echinops telfairi	ENSETEG00000003899	2 retrocopies	retro_etel_629, retro_etel_63,
Ictidomys tridecemlineatus	ENSSTOG00000004500	1 retrocopy	retro_itri_219 ,