RetrogeneDB ID: retro_itri_1420

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393481.1:3124960..3125266(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000011141
• Aliases: None
• Description: None

Sequence

>retro_itri_1420
TTAAGGTGGTATCAGCATCCTACAGAAGAAGAATTAAGAATTCTTGCAGGGAAGCAACAAAAAGGGAAAAGCAGAAAAGA
CAGGAAATATAATGGTCACATTGAAAATAAACCAGTAACCATTCCAAAGGATATTGACCTTCATCTAGAAACCATGTCAG
TTACAGAAGTGGATACTTTAGCATTGCATTACTTTCCAGAATACCAGTGGTTGGTGGATTTCACAGTGGCTGCTACAGTT
ATATATCTAGTAACTGAAGTCTACTACAGTCTTATGAAGCCTACACAGAAAATGAATATCACCTTA

Alignment

ORF - retro_itri_1420 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.12 %
• Parental protein coverage: 74.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRWYQHPTEEELRILAGKQQKGKSRKDRKYNGHIENKPLTIPKDIDLHLETKSVTEVDTLALHYFPEYQW
          LRWYQHPTEEELRILAGKQQKGKSRKDRKYNGHIENKP.TIPKDIDLHLET.SVTEVDTLALHYFPEYQW
Retrocopy LRWYQHPTEEELRILAGKQQKGKSRKDRKYNGHIENKPVTIPKDIDLHLETMSVTEVDTLALHYFPEYQW

Parental  LVDFTVAATVVYLVTEVYYSFMKPTQEMNISL
          LVDFTVAATV.YLVTEVYYS.MKPTQ.MNI.L
Retrocopy LVDFTVAATVIYLVTEVYYSLMKPTQKMNITL

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_1420 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1420 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010857	1 retrocopy	retro_cjac_2671,
Homo sapiens	ENSG00000164180	1 retrocopy	retro_hsap_560,
Gorilla gorilla	ENSGGOG00000005684	1 retrocopy	retro_ggor_506,
Macaca mulatta	ENSMMUG00000009319	1 retrocopy	retro_mmul_719,
Nomascus leucogenys	ENSNLEG00000013645	1 retrocopy	retro_nleu_2224,
Pan troglodytes	ENSPTRG00000017064	1 retrocopy	retro_ptro_419,
Ictidomys tridecemlineatus	ENSSTOG00000011141	1 retrocopy	retro_itri_1420 ,
Ictidomys tridecemlineatus	ENSSTOG00000027831	2 retrocopies	retro_itri_1419, retro_itri_1787,