RetrogeneDB ID: retro_itri_307

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393283.1:3152625..3152963(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000026027
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KIAA1143
• Ensembl ID: ENSSTOG00000010817
• Aliases: None
• Description: KIAA1143 [Source:HGNC Symbol;Acc:29198]

Sequence

>retro_itri_307
ATGAGCAAGTGGAACCAGGTGTTGTACAGGAGGCCTGCTGAACCCACCTTCCTGTCCTGCTTTAAGGAGCAAGTCTGGTA
CAGGGAGGGGCCCATCATAGAGACCAAGAGAATCCAGCCTCAGCTCCTGGATGAAGATGTTGATCACAGTGACAGCGATG
AACAGCCCCAAGAGGTGGTTTTAAAAAAGGAAGACCTGACAGCTGAAGAAGTCATGAAATTAAAGCAGAAATAAACGCTG
CAAAAACAGATGAAGAACCAGCTCCAGTTCACAGAAGAATCATGTATCAAAAACCAGTCAAGCGTCTCTCAGATGAAAAA
TATTCAGGTTTAACAGCA

Alignment

ORF - retro_itri_307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 73.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKRNQVSYVRPAEPAFLSRFKERVGYREGPTIESKRIQPQLPDEDADHSDQEDERPQVVVLKKGDLTAE
          MSK.NQV.Y.RPAEP.FLS.FKE.V.YREGP.IE.KRIQPQL.DED.DHSD..DE.PQ.VVLKK.DLTAE
Retrocopy MSKWNQVLYRRPAEPTFLSCFKEQVWYREGPIIETKRIQPQLLDEDVDHSD-SDEQPQEVVLKKEDLTAE

Parental  EVMK-IKAEIKAAKTDEEPAPTDGRIMYRKPVKRPSDEKYSGLTA
          EVMK.IKAEI.AAKTDEEPAP...RIMY.KPVKR.SDEKYSGLTA
Retrocopy EVMK<IKAEINAAKTDEEPAPVHRRIMYQKPVKRLSDEKYSGLTA

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_307 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_307 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014132	1 retrocopy	retro_cfam_2208,
Homo sapiens	ENSG00000163807	2 retrocopies	retro_hsap_1399, retro_hsap_2762,
Nomascus leucogenys	ENSNLEG00000005987	1 retrocopy	retro_nleu_666,
Oryctolagus cuniculus	ENSOCUG00000000929	2 retrocopies	retro_ocun_1601, retro_ocun_432,
Pongo abelii	ENSPPYG00000013954	1 retrocopy	retro_pabe_2250,
Pan troglodytes	ENSPTRG00000014824	1 retrocopy	retro_ptro_1869,
Pteropus vampyrus	ENSPVAG00000012438	2 retrocopies	retro_pvam_367, retro_pvam_458,
Sus scrofa	ENSSSCG00000011308	2 retrocopies	retro_sscr_844, retro_sscr_874,
Ictidomys tridecemlineatus	ENSSTOG00000010817	1 retrocopy	retro_itri_307 ,