RetrogeneDB ID: retro_fcat_1106

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:100198192..100198433(+)
• Located in intron of: ENSFCAG00000009649

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2D3
• Ensembl ID: ENSFCAG00000024918
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 3 [Source:HGNC Symbol;Acc:12476]

Sequence

>retro_fcat_1106
AAGGTTGCATCTACAACAAGAATTTATATCTAAATATTAACAGAAATGGCAGTAGTTTTCTTGGTATTTGAAGATCAGTG
ATCTCCTGCTTTAACTATTTCTAAAGTTCTTTTACCCCTTTGTTCACTGCTTTGTGACCCAAACCCAGATGACCCTAGCT
CCAGAGACTACATGGATCTATAAAACAGACAGAGATAAGTACAACAGAATATCTCGGGAATAAACTCAGAAGTATGCCAT
G

Alignment

ORF - retro_fcat_1106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.29 %
• Parental protein coverage: 55.78 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCD-PNPDDP-LVPEIARIYKTDRDK
          KVA.TTRIY...........L.....Q.SPALTISKVLL..CSLLCD.P.P..P.L.PE...IYKTDRDK
Retrocopy KVASTTRIYI*ILTEMAVVFL-VFEDQ*SPALTISKVLLPLCSLLCD<PKPR*P<LAPETTWIYKTDRDK

Parental  YNRISREWTQKYAM
          YNRISRE.TQKYAM
Retrocopy YNRISRE*TQKYAM

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	173.42 RPM
SRP017611_kidney	0.00 RPM	195.09 RPM
SRP017611_liver	0.00 RPM	151.33 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1106 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1106 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 17 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000018711	2 retrocopies	retro_cint_19, retro_cint_29,
Ciona savignyi	ENSCSAVG00000006136	1 retrocopy	retro_csav_18,
Erinaceus europaeus	ENSEEUG00000014658	3 retrocopies	retro_eeur_263, retro_eeur_566, retro_eeur_591,
Echinops telfairi	ENSETEG00000001291	3 retrocopies	retro_etel_1218, retro_etel_1998, retro_etel_36,
Felis catus	ENSFCAG00000007748	2 retrocopies	retro_fcat_1582, retro_fcat_913,
Felis catus	ENSFCAG00000008008	1 retrocopy	retro_fcat_369,
Felis catus	ENSFCAG00000024719	1 retrocopy	retro_fcat_623,
Felis catus	ENSFCAG00000024918	2 retrocopies	retro_fcat_1106 , retro_fcat_785,
Gorilla gorilla	ENSGGOG00000001368	2 retrocopies	retro_ggor_1156, retro_ggor_2321,
Mus musculus	ENSMUSG00000078578	11 retrocopies	retro_mmus_1818, retro_mmus_1895, retro_mmus_1913, retro_mmus_2293, retro_mmus_2635, retro_mmus_2643, retro_mmus_3119, retro_mmus_3636, retro_mmus_850, retro_mmus_875, retro_mmus_923,
Ornithorhynchus anatinus	ENSOANG00000005415	1 retrocopy	retro_oana_51,
Pongo abelii	ENSPPYG00000014967	1 retrocopy	retro_pabe_91,
Pteropus vampyrus	ENSPVAG00000015438	1 retrocopy	retro_pvam_234,
Sus scrofa	ENSSSCG00000024306	1 retrocopy	retro_sscr_783,
Sus scrofa	ENSSSCG00000029822	4 retrocopies	retro_sscr_1016, retro_sscr_672, retro_sscr_673, retro_sscr_918,
Ictidomys tridecemlineatus	ENSSTOG00000013481	6 retrocopies	retro_itri_1222, retro_itri_1474, retro_itri_1628, retro_itri_463, retro_itri_672, retro_itri_998,
Tupaia belangeri	ENSTBEG00000000270	5 retrocopies	retro_tbel_1336, retro_tbel_145, retro_tbel_1837, retro_tbel_262, retro_tbel_3134,