RetrogeneDB ID: retro_fcat_611

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:45265945..45266150(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS28
• Ensembl ID: ENSFCAG00000024931
• Aliases: None
• Description: ribosomal protein S28 [Source:HGNC Symbol;Acc:10418]

Sequence

>retro_fcat_611
ATGGACACAAACTGTGTGCAGTCCATCAAGTTGGCCAGGATCACCAAAGTGCTGGGCAGGACCAGCTCACAGGGACAGTG
CATGCAGGTGTGTGCGGAGTTCATTGGATGACATGAACCACTCCACCAACTTTGATGTGAAAGGCCCTGTGTGCAAGGGT
GACATGCTCACCCTACTGGAGTCAGAGCAAGAGGCTCGGAGACTG

Alignment

ORF - retro_fcat_611 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.57 %
• Parental protein coverage: 98.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEF-MDDTSRSIIRNVKGPVREGDVLTLLESEREARRL
          MDT..VQ.IKLAR.TKVLGRT.SQGQC.QV..EF..DD...S....VKGPV..GD.LTLLESE.EARRL
Retrocopy MDTNCVQSIKLARITKVLGRTSSQGQCMQVCAEF>LDDMNHSTNFDVKGPVCKGDMLTLLESEQEARRL

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	16.18 RPM
SRP017611_kidney	0.00 RPM	65.65 RPM
SRP017611_liver	0.00 RPM	23.15 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_611 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_611 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 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004917	1 retrocopy	retro_amel_1359,
Felis catus	ENSFCAG00000024931	3 retrocopies	retro_fcat_1130, retro_fcat_611 , retro_fcat_752,
Loxodonta africana	ENSLAFG00000029923	2 retrocopies	retro_lafr_168, retro_lafr_755,
Macaca mulatta	ENSMMUG00000028895	3 retrocopies	retro_mmul_122, retro_mmul_182, retro_mmul_807,
Monodelphis domestica	ENSMODG00000003890	1 retrocopy	retro_mdom_291,
Mus musculus	ENSMUSG00000067288	3 retrocopies	retro_mmus_2949, retro_mmus_3283, retro_mmus_91,
Oryctolagus cuniculus	ENSOCUG00000021484	2 retrocopies	retro_ocun_1230, retro_ocun_1799,
Rattus norvegicus	ENSRNOG00000042886	2 retrocopies	retro_rnor_95, retro_rnor_96,
Sus scrofa	ENSSSCG00000013597	3 retrocopies	retro_sscr_132, retro_sscr_191, retro_sscr_808,