RetrogeneDB ID: retro_fcat_401

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A2:122751780..122752125(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM254
• Ensembl ID: ENSFCAG00000026147
• Aliases: None
• Description: transmembrane protein 254 [Source:HGNC Symbol;Acc:25804]

Sequence

>retro_fcat_401
GGGTGGTGGCAGGAGGTAAGACGTATTTCCAGTGGGACAAACTCCTTTGGGTATTACATGTGGGTTGTCTTCTGGCATCA
GAGTATCCCTTATCACAGCCTAAGGCCCCTGGGCCCCTTCACTCAGTACTTGCTGGACCACCATTATCACACCCTTTTGT
ACAATGGGTATTGGCTCGCCTGGCTGATTCACATGGGACAGTCCTTGAATGTGACGGTTTTGTGCAAGTCTAAAACCATC
ACAAATGCTTGCACTCAACTACTCTTGTTCCTACAAACTTTCCTCTTTGGGATAGCATCTCTCTCCATCTTCATCGCTTA
TAGACCAAAACACCAAAAGCAAAGT

Alignment

ORF - retro_fcat_401 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.96 %
• Parental protein coverage: 78.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GYFRRARRLPSLVTVLALGYFAWVVFWPQSIPYQSLGPLGLFTQYLVDHH-HTLLRSGYWLAWLIHVGEA
          G.....RR..S.......GY..WVVFW.QSIPY.SL.PLG.FTQYL.DHH.HTLL..GYWLAWLIH.G..
Retrocopy GWWQEVRRISSGTN--SFGYYMWVVFWHQSIPYHSLRPLGPFTQYLLDHHYHTLLYNGYWLAWLIHMGQS

Parental  LYAMVLCKSKGITDGRAQVLWFLQTFLFGVASLSILIAYRPKRQKQT
          L...VLCKSK.IT....Q.L.FLQTFLFG.ASLSI.IAYRPK.QKQ.
Retrocopy LNVTVLCKSKTITNACTQLLLFLQTFLFGIASLSIFIAYRPKHQKQS

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	6.66 RPM
SRP017611_kidney	0.00 RPM	4.64 RPM
SRP017611_liver	0.00 RPM	8.69 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_401 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_401 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 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015748	3 retrocopies	retro_cfam_602, retro_cfam_635, retro_cfam_637,
Callithrix jacchus	ENSCJAG00000007670	1 retrocopy	retro_cjac_3839,
Dasypus novemcinctus	ENSDNOG00000024625	1 retrocopy	retro_dnov_555,
Felis catus	ENSFCAG00000026147	1 retrocopy	retro_fcat_401 ,
Myotis lucifugus	ENSMLUG00000007585	16 retrocopies	retro_mluc_1178, retro_mluc_2482, retro_mluc_2491, retro_mluc_2492, retro_mluc_2528, retro_mluc_2532, retro_mluc_2550, retro_mluc_2551, retro_mluc_2552, retro_mluc_2572, retro_mluc_2573, retro_mluc_2583, retro_mluc_2586, retro_mluc_2603, retro_mluc_2623, retro_mluc_766,
Macaca mulatta	ENSMMUG00000003015	1 retrocopy	retro_mmul_1583,
Mus musculus	ENSMUSG00000072676	1 retrocopy	retro_mmus_2102,
Oryctolagus cuniculus	ENSOCUG00000013679	1 retrocopy	retro_ocun_453,
Otolemur garnettii	ENSOGAG00000028898	1 retrocopy	retro_ogar_59,
Tarsius syrichta	ENSTSYG00000006920	1 retrocopy	retro_tsyr_103,
Tursiops truncatus	ENSTTRG00000006122	1 retrocopy	retro_ttru_454,