RetrogeneDB ID: retro_itri_1063

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393366.1:1031752..1032033(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXNL4A
• Ensembl ID: ENSSTOG00000022277
• Aliases: None
• Description: thioredoxin-like 4A [Source:HGNC Symbol;Acc:30551]

Sequence

>retro_itri_1063
TCAAACAAGCTCCAGCACCTGCACAATAGCTGGCAGGTGGACCAGGCCTTCCTCTGGAGGAGGACCTTATTGTGGTCAAT
TAGTTTGGACATGACTGGGACCCCACCTGCATAAAGATGGATGATGTTCCATAAAGTCTCATTGAAAAAATTTGAAGTTT
TGTTTTGTATCCTGTGGACATCACAGAAGTATCTGACTTCAAGAAAATATATGAGTTATACAATCCATATATCGTTATGC
TTTTCTATAGGAATAAGCACATCAGGATTGACTTGGGCACT

Alignment

ORF - retro_itri_1063 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 66.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SYMLPHLHNGWQVDQAIL-SEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFN
          S..L.HLHN.WQVDQA.L..EED..VV..FGHDWDPTC.KMD.V..S..EK...F.V.Y.VDITEV.DF.
Retrocopy SNKLQHLHNSWQVDQAFL<LEEDLIVVN*FGHDWDPTCIKMDDVP*SLIEKI*SF-VLYPVDITEVSDFK

Parental  KMYELYDPCTVMFFFRNKHIMIDLGT
          K.YELY.P..VM.F.RNKHI.IDLGT
Retrocopy KIYELYNPYIVMLFYRNKHIRIDLGT

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_1063 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1063 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010130	2 retrocopies	retro_cjac_2805, retro_cjac_3659,
Homo sapiens	ENSG00000141759	2 retrocopies	retro_hsap_2185, retro_hsap_4900,
Gorilla gorilla	ENSGGOG00000005285	2 retrocopies	retro_ggor_1731, retro_ggor_3060,
Loxodonta africana	ENSLAFG00000003190	1 retrocopy	retro_lafr_198,
Myotis lucifugus	ENSMLUG00000009188	1 retrocopy	retro_mluc_562,
Macaca mulatta	ENSMMUG00000001613	2 retrocopies	retro_mmul_2636, retro_mmul_913,
Nomascus leucogenys	ENSNLEG00000008378	2 retrocopies	retro_nleu_1268, retro_nleu_314,
Otolemur garnettii	ENSOGAG00000034753	1 retrocopy	retro_ogar_1751,
Pan troglodytes	ENSPTRG00000010136	1 retrocopy	retro_ptro_1663,
Rattus norvegicus	ENSRNOG00000017596	2 retrocopies	retro_rnor_1358, retro_rnor_2458,
Ictidomys tridecemlineatus	ENSSTOG00000022277	1 retrocopy	retro_itri_1063 ,
Tarsius syrichta	ENSTSYG00000009428	1 retrocopy	retro_tsyr_240,