RetrogeneDB ID: retro_fcat_1875

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: JH408686.1:1047996..1048230(-)
• Located in intron of: ENSFCAG00000029060

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKS2
• Ensembl ID: ENSFCAG00000022286
• Aliases: None
• Description: CDC28 protein kinase regulatory subunit 2 [Source:HGNC Symbol;Acc:2000]

Sequence

>retro_fcat_1875
GCCCACAAGCAGATCTATCAACTTGAACAAGTATTTCAACAAGCACTACGAGTACCAGCGTTTCATGTTACCCAGAGAAC
TTTCCTAACCAGTATCTAAAACCCATCTGATGTCTGAAGACCAGTGGAGGAGACCTGGTGTCCAACAGAGTCCAGGCTGG
GTTCATCACAGGATTCATGAGTCAGAATCACATATTCGTCTCTTAAATAACCTCTTCCAAAATATCAACAAAAA

Alignment

ORF - retro_fcat_1875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.5 %
• Parental protein coverage: 98.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AHKQIYYSD-KYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEPHILLFR
          AHKQIY....KYF..HYEY...MLPRELS..V.KTHLMSE..WRR.GVQQS.GWVH..IHE.E.HI.L..
Retrocopy AHKQIYQLE>KYFNKHYEYQRFMLPRELS*PVSKTHLMSEDQWRRPGVQQSPGWVHHRIHESESHIRLLN

Parental  R-PLPKEQQK
          ..PLPK.QQK
Retrocopy N<PLPKYQQK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	8.84 RPM
SRP017611_kidney	0.00 RPM	13.09 RPM
SRP017611_liver	0.00 RPM	11.02 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1875 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1875 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus 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 18 parental genes, and 49 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	ENSFCAG00000001347	1 retrocopy	retro_fcat_1041,
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,