RetrogeneDB ID: retro_fcat_246

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:109748839..109749531(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPA2
• Ensembl ID: ENSFCAG00000023073
• Aliases: None
• Description: non imprinted in Prader-Willi/Angelman syndrome 2 [Source:HGNC Symbol;Acc:17044]

Sequence

>retro_fcat_246
CTTCTGCAAGTTGCCAGGAAAGGCTCCAAGAGAGCAGGTCAAGGTGGCCATGCATATCTTAAAGAATCATTGTGGTGGGC
TGGATTGCTATCAATGGGAGCAGGTGAGGTGGCCAACTTTGCTGCATATGCCTTTGCACCAGCCACCCTTGTGACTTCAT
TAGGAGCTCTCAGCATCCCAGTAAGTGCATCCTTTCTTCATACACCCACTCTAAATGAAAGACATAATTTTCATGGGAAA
ATTGGTTGTTTGCTAAGTATTCTAGAATCTATAGTTATGGTCATTCATGCTCTAGAGAAGAGGAGATCAAGACTTCAAAC
GAAATGTCTCATAAGCTGGGAGATCAAGGTTTTGTAGTCTTTGCAACCCTTGTGGTCATTGTGTCATTGATATTAATCTT
TGAGGTGGGACCTTGCCATAGACAGAAAAACATTCTTGTGTGCATAGAAATCTGCTCTGTAATCAGAGTGTTTTTGTTGT
CCTGTGTTAAGGGCTTGGGCCTTGATATCAAAGAGATGTTTGCTGGAAAGCCTGTGTTGTGACATCTGGCCAGGATTCTG
CTGCTGAGCCTTATAGTCTATGAGAGCACACAGATTAATTACCTGGGCAGGGCCCTGGGTATATTCAATACTTTCATTCT
CACTTCAGTATATTACATATTTTTTACAACCTCAGTTTGAACTGGTTCAGCT

Alignment

ORF - retro_fcat_246 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.82 %
• Parental protein coverage: 64.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLRLARKGSMRAGQGGHAYLKEWLWWAGLLSMGAGEVVNFAAYAFAPATLVTPLGALSVLVSA-ILSSYF
          LL..ARKGS.RAGQGGHAYLKE.LWWAGLLSMGAGEV.NFAAYAFAPATLVT.LGALS..VSA..L....
Retrocopy LLQVARKGSKRAGQGGHAYLKESLWWAGLLSMGAGEVANFAAYAFAPATLVTSLGALSIPVSASFLHTPT

Parental  LNERLNLHGKIGWLLSILGSTVMVIHA-PKEEEIETLNEMSHKLGDPGFVVFATLVVIVSLILIFVVGPR
          LNER.N.HGKIG.LLSIL.S.VMVIHA...EEEI.T.NEMSHKLGD.GFVVFATLVVIVSLILIF.VGP.
Retrocopy LNERHNFHGKIGCLLSILESIVMVIHA<SREEEIKTSNEMSHKLGDQGFVVFATLVVIVSLILIFEVGPC

Parental  HGRTNILVYITICSVIGAFSVSCVKGLGIAIKELFAGKPVLRHPLAWILLLSLIVCVSTQINYLNRALDI
          H...NILV.I.ICSVI..F..SCVKGLG..IKE.FAGKPVL.H.LA.ILLLSLIV..STQINYL.RAL.I
Retrocopy HRQKNILVCIEICSVIRVFLLSCVKGLGLDIKEMFAGKPVL*H-LARILLLSLIVYESTQINYLGRALGI

Parental  FNTSIVTPIYYVFFTASVLTCSA
          FNT.I.T..YY.FFT.SV.T.SA
Retrocopy FNTFILTSVYYIFFTTSV*TGSA

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	38.68 RPM
SRP017611_kidney	0.00 RPM	71.32 RPM
SRP017611_liver	0.00 RPM	26.99 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_246 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_246 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013824	1 retrocopy	retro_amel_1163,
Choloepus hoffmanni	ENSCHOG00000005553	1 retrocopy	retro_chof_9,
Callithrix jacchus	ENSCJAG00000005448	1 retrocopy	retro_cjac_1506,
Equus caballus	ENSECAG00000006379	1 retrocopy	retro_ecab_656,
Felis catus	ENSFCAG00000023073	1 retrocopy	retro_fcat_246 ,
Macaca mulatta	ENSMMUG00000003892	1 retrocopy	retro_mmul_1510,
Mus musculus	ENSMUSG00000030452	1 retrocopy	retro_mmus_3551,
Oryctolagus cuniculus	ENSOCUG00000010746	3 retrocopies	retro_ocun_1581, retro_ocun_773, retro_ocun_809,
Ictidomys tridecemlineatus	ENSSTOG00000004003	3 retrocopies	retro_itri_1847, retro_itri_347, retro_itri_388,
Vicugna pacos	ENSVPAG00000000671	1 retrocopy	retro_vpac_285,