RetrogeneDB ID: retro_fcat_727

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B2:109471562..109471914(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000028856
• Aliases: None
• Description: None

Sequence

>retro_fcat_727
CCCAGATGTTCCAAGATCCACCTGCCAGGGTTTATGCATCAGGCTGAAGCTCTGAAGGCCAAGGGGGTCCAGGTGGTAGC
ATATCTGAGTGTTAATGATGTCTTTGTAGCTGAAGAGTGGGGACAAGCTCACAACTCTGGAGACAAGGTTAGGCTCTTGG
CTGACTCCCTTGGGACCTTTAGGAAGGAGACAGATTTGTTACTAGGTGATTGATTCATTGGTATCTCTCTTTGGAAATCC
ACTGCTCAAGAGGTTCTCCATGGTGGTAGAGGATGGTATAGTGAAGTCTCTGAATGTGGAGCTGGATGATAGAGGCTTCA
TCTGCAGCCTGGCACCCAACATCATCTCACAG

Alignment

ORF - retro_fcat_727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.27 %
• Parental protein coverage: 71.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PGCSKTHLPGFVEQAEALKAKGAQVIACLSVNDVFVTTEWGRAHNSGGKVRLLADPTGAFGKETG-LLLD
          P.CSK.HLPGF..QAEALKAKG.QV.A.LSVNDVFV..EWG.AHNSG.KVRLLAD..G.F.KET..LL.D
Retrocopy PRCSKIHLPGFMHQAEALKAKGVQVVAYLSVNDVFVAEEWGQAHNSGDKVRLLADSLGTFRKETDLLLGD

Parental  -DSLVSLFGNRRLKRFSMVVEDGVVKSLNVEPDGTGLTCSLASNIISQ
          .DSLVSLFGN..LKRFSMVVEDG.VKSLNVE.D..G..CSLA.NIISQ
Retrocopy >DSLVSLFGNPLLKRFSMVVEDGIVKSLNVELDDRGFICSLAPNIISQ

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	84.59 RPM
SRP017611_kidney	0.00 RPM	184.37 RPM
SRP017611_liver	0.00 RPM	31.44 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_727 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_727 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 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008648	1 retrocopy	retro_btau_1364,
Callithrix jacchus	ENSCJAG00000018014	1 retrocopy	retro_cjac_3013,
Dasypus novemcinctus	ENSDNOG00000004647	1 retrocopy	retro_dnov_2664,
Equus caballus	ENSECAG00000017747	2 retrocopies	retro_ecab_823, retro_ecab_844,
Echinops telfairi	ENSETEG00000000264	3 retrocopies	retro_etel_1821, retro_etel_662, retro_etel_740,
Felis catus	ENSFCAG00000028856	3 retrocopies	retro_fcat_1189, retro_fcat_410, retro_fcat_727 ,
Homo sapiens	ENSG00000126432	1 retrocopy	retro_hsap_408,
Gorilla gorilla	ENSGGOG00000001337	1 retrocopy	retro_ggor_404,
Loxodonta africana	ENSLAFG00000025661	2 retrocopies	retro_lafr_132, retro_lafr_250,
Macaca mulatta	ENSMMUG00000013397	1 retrocopy	retro_mmul_504,
Nomascus leucogenys	ENSNLEG00000005003	2 retrocopies	retro_nleu_1007, retro_nleu_2228,
Procavia capensis	ENSPCAG00000010811	1 retrocopy	retro_pcap_144,
Pongo abelii	ENSPPYG00000003106	1 retrocopy	retro_pabe_310,
Pan troglodytes	ENSPTRG00000003835	1 retrocopy	retro_ptro_313,
Sus scrofa	ENSSSCG00000013030	2 retrocopies	retro_sscr_1041, retro_sscr_888,