RetrogeneDB ID: retro_fcat_1964

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:13639844..13640156(-)
• Located in intron of: ENSFCAG00000000186

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHP1
• Ensembl ID: ENSFCAG00000006346
• Aliases: None
• Description: calcineurin-like EF-hand protein 1 [Source:HGNC Symbol;Acc:17433]

Sequence

>retro_fcat_1964
CAGCTGACTCCAGAACTTGTCATCCACCCACCAGGGGACTGGCTCACTGGTGCCTTCTTTTCAGAGGGGGAAGACCAGGT
CAACTTCCACTGATTCATAAAAACTTTGGCTCATTTCCAATCCACTGAATATAGTGCAAGGAGCGAAGGTAAGAATGAAC
CAGAACCACAGAACAGCTGAAGCAACGTATTATACTTTGCTTTTCAGCTCTATGATTTGGATAAAGATGACAAGATCACC
TGCAATAAGCTGTCCCAGGTGCTATGCATGATGGTTGGAATGGTTATCTCACATGAGCAACTGAGCAGCATC

Alignment

ORF - retro_fcat_1964 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.54 %
• Parental protein coverage: 53.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRIPELAINPLGDRIINAFFPEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRL
          Q..PEL.I.P.GD....AFF.EGEDQVNF..F..TLAHF...E....S...N.PEP.NS.SN.L.FAF.L
Retrocopy QLTPELVIHPPGDWLTGAFFSEGEDQVNFH*FIKTLAHFQSTEYSARSEGKNEPEPQNS*SNVLYFAFQL

Parental  YDLDKDDKISRDELLQVLRMMVGVNISDEQLGSI
          YDLDKDDKI....L.QVL.MMVG..IS.EQL.SI
Retrocopy YDLDKDDKITCNKLSQVLCMMVGMVISHEQLSSI

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	0.11 RPM	55.89 RPM
SRP017611_kidney	0.00 RPM	24.32 RPM
SRP017611_liver	0.00 RPM	21.33 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1964 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1964 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027173	1 retrocopy	retro_btau_1785,
Callithrix jacchus	ENSCJAG00000020761	1 retrocopy	retro_cjac_2396,
Equus caballus	ENSECAG00000019751	1 retrocopy	retro_ecab_1099,
Felis catus	ENSFCAG00000006346	1 retrocopy	retro_fcat_1964 ,
Felis catus	ENSFCAG00000028482	1 retrocopy	retro_fcat_1639,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Loxodonta africana	ENSLAFG00000014743	3 retrocopies	retro_lafr_221, retro_lafr_795, retro_lafr_838,
Oryctolagus cuniculus	ENSOCUG00000013832	1 retrocopy	retro_ocun_68,
Otolemur garnettii	ENSOGAG00000013099	2 retrocopies	retro_ogar_2442, retro_ogar_628,
Procavia capensis	ENSPCAG00000005419	1 retrocopy	retro_pcap_240,
Pongo abelii	ENSPPYG00000006370	2 retrocopies	retro_pabe_2749, retro_pabe_2925,
Pteropus vampyrus	ENSPVAG00000003150	1 retrocopy	retro_pvam_1207,