RetrogeneDB ID: retro_itri_866

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393335.1:5066658..5066966(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000022984
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: POLE3
• Ensembl ID: ENSSTOG00000027365
• Aliases: None
• Description: polymerase (DNA directed), epsilon 3, accessory subunit [Source:HGNC Symbol;Acc:13546]

Sequence

>retro_itri_866
ATGGCGGAGAGGCCAGAGGACTTAAACCTGCCCAGTGCTGTCATCACCAGGATCATTAAAGAGGCGCTCCCGGAAGGTGT
CAACATCTCCAAGGAGGCCCAGAGCGCCATCTCCTGCACCGCCAGTGTCTTCGTGCTGTATGCCACAAGCTGTGCCAACA
ACTTTGCAATGAAAGGGAAACGCAAGACGCTCAATGCCAGTGATGTGCTCTCAGCCATGGAAGAGATGGAGTTCCAGCGG
TTCATTACCCCTTAAAAGAAGCTCTGGAAGCTTATAGGCGGGAACAGAAAGGTAAGAAGGAAGCTTCA

Alignment

ORF - retro_itri_866 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.23 %
• Parental protein coverage: 70.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAERPEDLNLPNAVITRIIKEALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVL
          MAERPEDLNLP.AVITRIIKEALP.GVNISKEA.SAIS..ASVFVLYATSCANNFAMKGKRKTLNASDVL
Retrocopy MAERPEDLNLPSAVITRIIKEALPEGVNISKEAQSAISCTASVFVLYATSCANNFAMKGKRKTLNASDVL

Parental  SAMEEMEFQRFITP-LKEALEAYRREQKGKKEAS
          SAMEEMEFQRFITP.LKEALEAYRREQKGKKEAS
Retrocopy SAMEEMEFQRFITP<LKEALEAYRREQKGKKEAS

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_866 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_866 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017917	1 retrocopy	retro_cjac_4121,
Cavia porcellus	ENSCPOG00000000313	1 retrocopy	retro_cpor_355,
Dipodomys ordii	ENSDORG00000003073	2 retrocopies	retro_dord_526, retro_dord_652,
Monodelphis domestica	ENSMODG00000004358	3 retrocopies	retro_mdom_1680, retro_mdom_1920, retro_mdom_647,
Mus musculus	ENSMUSG00000028394	2 retrocopies	retro_mmus_124, retro_mmus_555,
Pteropus vampyrus	ENSPVAG00000004717	1 retrocopy	retro_pvam_302,
Rattus norvegicus	ENSRNOG00000015392	1 retrocopy	retro_rnor_55,
Ictidomys tridecemlineatus	ENSSTOG00000005279	1 retrocopy	retro_itri_1851,
Ictidomys tridecemlineatus	ENSSTOG00000027365	1 retrocopy	retro_itri_866 ,
Tupaia belangeri	ENSTBEG00000005211	1 retrocopy	retro_tbel_4052,