RetrogeneDB ID: retro_itri_928

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393345.1:8345190..8345466(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000015971
• Aliases: None
• Description: None

Sequence

>retro_itri_928
CTCAAGGTGAAAGGCTGGGGCTGCCCTGCTTCTGGGAGGCCTTGCTGGGAATTACCTGAGCTCAGAGAAGACAGAGTCTA
CCTGATGGAGCTTCCAGGGCTCTGGTGGATGAAGTAGAGTGGAAAATTGCCCCCGACACTTCCCAAGACTTTCAGATGGG
GCTTTGCAGATAGATCCAGTGGGCAGCCAGTCAGTTTTGGAGGTGCCTTAGCCTGCTCAGAGGCCCAGCTCACAGAGTGG
CGAGAGGAGGCAGGTGACCGGGTGAAGGCTGTGGGG

Alignment

ORF - retro_itri_928 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.7 %
• Parental protein coverage: 51.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MKGWGW-LALLLG-ALLGTASARRSQDLHCGACRALVDELEWEIAQVDPKKTIQM-GSFRINPDGSQSVV
          .K..GW..ALLLG.ALLG...A.R.Q.L..GA.RALVDE.EW.IA..D.....QM.G...I.P.GSQSV.
Retrocopy LKVKGW>AALLLG>ALLGIT*AQRRQSLPDGASRALVDEVEWKIAP-DTSQDFQM<GALQIDPVGSQSVL

Parental  EVP-YARSEAHLTELLEEVCDRMKEYG
          EVP..A.SEA.LTE..EE..DR.K..G
Retrocopy EVP<LACSEAQLTEWREEAGDRVKAVG

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_928 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_928 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011259	1 retrocopy	retro_cjac_1188,
Dasypus novemcinctus	ENSDNOG00000010925	1 retrocopy	retro_dnov_444,
Mustela putorius furo	ENSMPUG00000001366	1 retrocopy	retro_mputfur_930,
Ictidomys tridecemlineatus	ENSSTOG00000015971	1 retrocopy	retro_itri_928 ,