RetrogeneDB ID: retro_fcat_580

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:149294814..149295207(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000024316
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF4H
• Ensembl ID: ENSFCAG00000029386
• Aliases: None
• Description: eukaryotic translation initiation factor 4H [Source:HGNC Symbol;Acc:12741]

Sequence

>retro_fcat_580
GTCCTACAGCAGCTCTGGCACGGCAGAGGGTCCTGCGGCAGTGCTTATGGCCATGGTTCCCATAGCCAGAAGGAGATGCC
CACAGAGCCCCGCTACACAGCATATGTAGGAAATCTACCTTTTAATACAGTTCAGGGCGACACAGATGCTATCTTTAAGG
ATCTCAGCATAAGGAGTGTACTGCTAGTCAGAGACAAAAACACAGACAAATTCTGCTATGTAGAATTTGATGAGGTGGAT
TCCCATAATGAAGGCTTGACACATGATGGTGCATGGTTGGGTGATCAGTCACTTCGTGCGGACATTGCAGAAGACACAAA
ACAAGATAAAAGTGGCTTTGGATTCAGGAAAGGTGGACCGGATGACAGAGGCTGTGCTCGCAGTGAGGACACG

Alignment

ORF - retro_fcat_580 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.19 %
• Parental protein coverage: 54.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VIYSPWWGGGSESRSRGSAGGHGSRSQKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDK
          V....W.G.G....S.GSA.GHGS.SQKE.PTEP.YTAYVGNLPFNTVQGD.DAIFKDLSIRSV.LVRDK
Retrocopy VLQQLWHGRG----SCGSAYGHGSHSQKEMPTEPRYTAYVGNLPFNTVQGDTDAIFKDLSIRSVLLVRDK

Parental  DTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKGGFGFRKGGPDDRGMGGSRES
          .TDKF...CYVEFDEVDS..E.LT.DGA.LGD.SLR.DIAE..KQDK.GFGFRKGGPDDRG...S...
Retrocopy NTDKF---CYVEFDEVDSHNEGLTHDGAWLGDQSLRADIAEDTKQDKSGFGFRKGGPDDRGCARSEDT

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	58.53 RPM
SRP017611_kidney	0.00 RPM	40.91 RPM
SRP017611_liver	0.00 RPM	25.58 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_580 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_580 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002525	2 retrocopies	retro_chof_1279, retro_chof_1903,
Felis catus	ENSFCAG00000029386	1 retrocopy	retro_fcat_580 ,
Gorilla gorilla	ENSGGOG00000005284	1 retrocopy	retro_ggor_1598,
Macaca mulatta	ENSMMUG00000006205	2 retrocopies	retro_mmul_2634, retro_mmul_619,
Mus musculus	ENSMUSG00000040731	1 retrocopy	retro_mmus_3659,
Oryctolagus cuniculus	ENSOCUG00000017685	1 retrocopy	retro_ocun_1475,
Otolemur garnettii	ENSOGAG00000028051	1 retrocopy	retro_ogar_2796,
Pongo abelii	ENSPPYG00000017489	2 retrocopies	retro_pabe_1879, retro_pabe_1988,
Pan troglodytes	ENSPTRG00000019287	1 retrocopy	retro_ptro_1489,
Rattus norvegicus	ENSRNOG00000001454	1 retrocopy	retro_rnor_2924,
Tupaia belangeri	ENSTBEG00000009558	2 retrocopies	retro_tbel_1636, retro_tbel_2470,