RetrogeneDB ID: retro_fcat_1815

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F2:44465283..44465628(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC11C
• Ensembl ID: ENSFCAG00000006501
• Aliases: None
• Description: SEC11 homolog C (S. cerevisiae) [Source:HGNC Symbol;Acc:23400]

Sequence

>retro_fcat_1815
CTTCTGCTCCTAACAAATTTCAGGGCAACCCTAGTGGAATTGGTGAAATAGTCATTTTTAAAATTGAATGATTTGATACT
CCAATAGTTCACAGAGTAATCAAAGTTCAAGAAAAAGATAATGAAGACATCAGGTTTCTAACTAAAGGAGATAATAATGA
AGTTGATGATAGAGGGGCTTACACAAACAAGGCCACAACTAGCTTGAAAAGAAAGATGGGGTGGGGGAGGAGTTACAGGG
TTTTTACCGTATGTTAGCATGGCCACCGTAATAATGAATGACTATCCAAACTTCAGGTATGTTCCTTTGGTTCTAATGAG
TACCTATGTGTTACTAAAACATGAA

Alignment

ORF - retro_fcat_1815 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.25 %
• Parental protein coverage: 59.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLFLTNFRE-DPIRAGEIVVFKVEGRDIPIVHRVIKVHEKDNGDIKFLTKGDNNEVDDRGLY-KEGQNWL
          LL.LTNFR...P...GEIV.FK.E..D.PIVHRVIKV.EKDN.DI.FLTKGDNNEVDDRG.Y.......L
Retrocopy LLLLTNFRA<NPSGIGEIVIFKIE*FDTPIVHRVIKVQEKDNEDIRFLTKGDNNEVDDRGAYTNKATTSL

Parental  EKKDVVGRA-RGFLPYVGMVTIIMNDYPKFKYALLAVMGAYVLLKRE
          ..K...GR...GFLPYV.M.T.IMNDYP.F.Y..L..M..YVLLK.E
Retrocopy KRKMGWGRS>TGFLPYVSMATVIMNDYPNFRYVPLVLMSTYVLLKHE

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	18.02 RPM
SRP017611_kidney	0.00 RPM	21.23 RPM
SRP017611_liver	0.00 RPM	14.86 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1815 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1815 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 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017024	3 retrocopies	retro_ecab_1009, retro_ecab_455, retro_ecab_989,
Echinops telfairi	ENSETEG00000005115	2 retrocopies	retro_etel_1081, retro_etel_1139,
Felis catus	ENSFCAG00000006501	1 retrocopy	retro_fcat_1815 ,
Felis catus	ENSFCAG00000029786	2 retrocopies	retro_fcat_1178, retro_fcat_1908,
Microcebus murinus	ENSMICG00000016052	1 retrocopy	retro_mmur_271,
Monodelphis domestica	ENSMODG00000020427	2 retrocopies	retro_mdom_1517, retro_mdom_377,
Oryctolagus cuniculus	ENSOCUG00000009204	2 retrocopies	retro_ocun_738, retro_ocun_895,
Otolemur garnettii	ENSOGAG00000002570	1 retrocopy	retro_ogar_400,
Pteropus vampyrus	ENSPVAG00000002950	2 retrocopies	retro_pvam_620, retro_pvam_869,
Sus scrofa	ENSSSCG00000004912	1 retrocopy	retro_sscr_775,
Tupaia belangeri	ENSTBEG00000014804	1 retrocopy	retro_tbel_2357,
Tursiops truncatus	ENSTTRG00000007676	5 retrocopies	retro_ttru_1278, retro_ttru_1508, retro_ttru_1780, retro_ttru_1916, retro_ttru_490,