RetrogeneDB ID: retro_itri_597

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393305.1:4200683..4201143(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000001385
• Aliases: None
• Description: None

Sequence

>retro_itri_597
ACAGTCACCTGGGAAGAGCAAAATAACCGGGCTGAGAGAAATGGGGGATATGCTAAAACAGAAACTAGCTGATATGAAAG
CACAAAATTACATGGCCAGAGTCTTCACTCACTGGAGGGCAGGATGTCTTGTCAGTATAAATCCAACAGCTCCTGGCAGT
TTGGCTTCAATGGACAGACGTGGCTCCACTTTGGCTCAGATAGCAGGTGTACAGAGGTTCATCCTGGGTCCAACTGGATG
AAAGAAAATGTGGGGAAATGACAAGGAGGTGACTGAGTTCTTACACAAGACCTCAATGGGTGACTATAAAACCTGGCTTC
AGAAGTTTTTGGTGCAGTGAGAAGCACAGCTGGAGCCCACAGGACCTTCGATTGCCACTCTCAACAAAGCCTTTCAAGAA
TCCACAGCCATCACCCTTATTTCCTCGGCCCTGCTGTGGATCCTCACCTGTTTTATCCAC

Alignment

ORF - retro_itri_597 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.08 %
• Parental protein coverage: 70.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TVTWEEQK-ATLRDMGDMLKQKLADTKAENDMAK-GLHILEGRMRCQLKSSGFTSGSWQFGFNGQMWLRF
          TVTWEEQ....LR.MGDMLKQKLAD.KA.N.MA...LH.LEGRM.CQ.KS......SWQFGFNGQ.WL.F
Retrocopy TVTWEEQN>TGLREMGDMLKQKLADMKAQNYMAR<SLHSLEGRMSCQYKSNS----SWQFGFNGQTWLHF

Parental  DSDNRRWTKVHPGSNRMKEK-WEDDREMTKFLHKTSMGDCRTWLEKFLVEWKTELEPTGPSSAIINRVSQ
          .SD.R..T.VHPGSN.MKE..W..D.E.T.FLHKTSMGD..TWL.KFLV.....LEPTGPS.A..N...Q
Retrocopy GSDSR-CTEVHPGSNWMKEN>WGNDKEVTEFLHKTSMGDYKTWLQKFLVQ*EAQLEPTGPSIATLNKAFQ

Parental  ESTASTLVPSALLLILTCFIH
          ESTA.TL..SALL.ILTCFIH
Retrocopy ESTAITLISSALLWILTCFIH

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_597 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_597 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
Canis familiaris	ENSCAFG00000000399	2 retrocopies	retro_cfam_1528, retro_cfam_432,
Myotis lucifugus	ENSMLUG00000025468	1 retrocopy	retro_mluc_1324,
Ictidomys tridecemlineatus	ENSSTOG00000001385	1 retrocopy	retro_itri_597 ,