RetrogeneDB ID: retro_itri_1449

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393492.1:2776879..2777122(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000019436
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HN1
• Ensembl ID: ENSSTOG00000015171
• Aliases: None
• Description: hematological and neurological expressed 1 [Source:HGNC Symbol;Acc:14569]

Sequence

>retro_itri_1449
ATGACCAACACCAACACCTTCAAGGGTTTTGACCCTAAGATCAGGAATAGCTCCTGGATTTTGCAGCCTCCTTGGGCTGG
TGGATCCAATTTCTCATTAGGATTTGATGAACCAACAGAATCATCCATGAGAAAGAATAAAATGGCCTCTAGCATCTTTG
GAACACCTGAAGAAAATCCCCCTTCTTGGGCCAAGTTGACAGATGCCAAAGATAGTGGTGGAAGCAAAGATTTGGAATCA
TCT

Alignment

ORF - retro_itri_1449 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.54 %
• Parental protein coverage: 51.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTTTTFKGVDPNSRNSSRVLRPP-GGGSNFSLGFDEPTEQPVRKNKMASSIFGTPEENPPSWAKSAGAK
          MT.T.TFKG.DP..RNSS..L.PP..GGSNFSLGFDEPTE...RKNKMASSIFGTPEENPPSWAK...AK
Retrocopy MTNTNTFKGFDPKIRNSSWILQPPWAGGSNFSLGFDEPTESSMRKNKMASSIFGTPEENPPSWAKLTDAK

Parental  SSGGREDLESS
          .SGG..DLESS
Retrocopy DSGGSKDLESS

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_1449 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1449 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 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014553	1 retrocopy	retro_cjac_2715,
Echinops telfairi	ENSETEG00000013294	1 retrocopy	retro_etel_89,
Homo sapiens	ENSG00000189159	1 retrocopy	retro_hsap_2343,
Gorilla gorilla	ENSGGOG00000013996	1 retrocopy	retro_ggor_1780,
Mustela putorius furo	ENSMPUG00000013971	1 retrocopy	retro_mputfur_1200,
Mus musculus	ENSMUSG00000020737	6 retrocopies	retro_mmus_1096, retro_mmus_2442, retro_mmus_2574, retro_mmus_3706, retro_mmus_864, retro_mmus_934,
Nomascus leucogenys	ENSNLEG00000000610	1 retrocopy	retro_nleu_348,
Oryctolagus cuniculus	ENSOCUG00000002950	2 retrocopies	retro_ocun_1647, retro_ocun_457,
Ochotona princeps	ENSOPRG00000010887	2 retrocopies	retro_opri_537, retro_opri_88,
Pan troglodytes	ENSPTRG00000024246	1 retrocopy	retro_ptro_1715,
Rattus norvegicus	ENSRNOG00000003661	2 retrocopies	retro_rnor_1794, retro_rnor_454,
Ictidomys tridecemlineatus	ENSSTOG00000015171	1 retrocopy	retro_itri_1449 ,