RetrogeneDB ID: retro_itri_1306

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393434.1:4108591..4108817(-)
• Located in intron of: ENSSTOG00000013888

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKS2
• Ensembl ID: ENSSTOG00000000048
• Aliases: None
• Description: CDC28 protein kinase regulatory subunit 2 [Source:HGNC Symbol;Acc:2000]

Sequence

>retro_itri_1306
CATAAGTAGATCTACTGCTCTAATAAGTATTTTGATGATCACTACAAGTACCAGCATGTCATGTTACCCACAGAACTTTC
CAAAGGTACCCAAAACTCATTTAACGTCTGAAGAGGAGTGGAGGAGACTTGGTGTCCAACAGAGTCTAGGCTGGGCCCAT
TACATGATTCGTGAACCAGAGCCACATATTTTTCTTTTTAGATGACCTCTTCTAGAAGAGTAACAA

Alignment

ORF - retro_itri_1306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.03 %
• Parental protein coverage: 96.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HKQIYYSDKYFDEHYEYRHVML-PRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEPHILLFRR
          HK.IY.S.KYFD.HY.Y.HVML.P....K.VPKTHL.SEEEWRRLGVQQSLGW.HYMI.EPEPHI.LFR.
Retrocopy HK*IYCSNKYFDDHYKYQHVML>PQNFPK-VPKTHLTSEEEWRRLGVQQSLGWAHYMIREPEPHIFLFR*

Parental  PLPKEQQ
          PL..E.Q
Retrocopy PLLEE*Q

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_1306 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1306 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 17 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007792	1 retrocopy	retro_cjac_261,
Dasypus novemcinctus	ENSDNOG00000009427	8 retrocopies	retro_dnov_1200, retro_dnov_1527, retro_dnov_195, retro_dnov_1984, retro_dnov_2530, retro_dnov_2532, retro_dnov_585, retro_dnov_755,
Erinaceus europaeus	ENSEEUG00000004384	7 retrocopies	retro_eeur_183, retro_eeur_255, retro_eeur_293, retro_eeur_551, retro_eeur_632, retro_eeur_639, retro_eeur_640,
Felis catus	ENSFCAG00000022286	1 retrocopy	retro_fcat_1875,
Homo sapiens	ENSG00000123975	1 retrocopy	retro_hsap_4183,
Macaca mulatta	ENSMMUG00000012534	1 retrocopy	retro_mmul_269,
Mus musculus	ENSMUSG00000062248	4 retrocopies	retro_mmus_1356, retro_mmus_1470, retro_mmus_2392, retro_mmus_409,
Nomascus leucogenys	ENSNLEG00000008729	1 retrocopy	retro_nleu_1793,
Otolemur garnettii	ENSOGAG00000028843	1 retrocopy	retro_ogar_798,
Ochotona princeps	ENSOPRG00000007583	3 retrocopies	retro_opri_111, retro_opri_1122, retro_opri_912,
Pongo abelii	ENSPPYG00000025843	1 retrocopy	retro_pabe_57,
Pan troglodytes	ENSPTRG00000021093	1 retrocopy	retro_ptro_2837,
Pteropus vampyrus	ENSPVAG00000011011	3 retrocopies	retro_pvam_1297, retro_pvam_1307, retro_pvam_605,
Rattus norvegicus	ENSRNOG00000014130	5 retrocopies	retro_rnor_1209, retro_rnor_1909, retro_rnor_2742, retro_rnor_279, retro_rnor_402,
Sorex araneus	ENSSARG00000002443	1 retrocopy	retro_sara_213,
Sus scrofa	ENSSSCG00000021161	2 retrocopies	retro_sscr_458, retro_sscr_675,
Ictidomys tridecemlineatus	ENSSTOG00000000048	7 retrocopies	retro_itri_1058, retro_itri_1306 , retro_itri_1429, retro_itri_1632, retro_itri_269, retro_itri_585, retro_itri_774,