RetrogeneDB ID: retro_fcat_1043

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:73142390..73142875(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP4C
• Ensembl ID: ENSFCAG00000014171
• Aliases: None
• Description: protein phosphatase 4, catalytic subunit [Source:HGNC Symbol;Acc:9319]

Sequence

>retro_fcat_1043
CTGCACGCTAAGGCAGGAGAGATCTTGGTAAAGGAGACCAATGTACAGAGGGTGGAGTCGCGGGTCACAATATGTGGTGA
CATCCATGGACAACTCTATGACTTCAAGGAGCTGTTCAGTGTGGGTGGTAAGACCCCGAGACCAACTACCTTTTCATGAG
AGACTGTATGGAACATGATTTCTAGGCATTGAAACATTCCTCCTGCTGCTGGTACTTAATGTTTAATATAATGACCACAT
CACCAAGATCCTGGGGAACCACTAGAGTTGCCAGATCCCCCAAGTCTATGGCTTCTTTGCTGAGTGCCTGTGAGAATATG
ATTTGGTGACCACATGGTGCTACTGCCCTGAGCTCTTTTGACTACATCAGTCTGTCAGCCATCATTAATGGCAATCTTTT
GCGTGCACGGGTACTTTCTCCCTCCATCCAGACTCTAGACCAGATTCAGATGACTGACTGAAAGCAAGAGGTGCCTCATG
AGGGG

Alignment

ORF - retro_fcat_1043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.46 %
• Parental protein coverage: 53.09 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LCAKAREILVEESNVQRVDSPVTVCGDIHGQFYDLKELFRVGGDVP-ETNYLFMGDFVDRGF-YSVETFL
          L.AKA.EILV.E.NVQRV.S.VT.CGDIHGQ.YD.KELF.VGG..P.ETNYLFM.D.....F....ETFL
Retrocopy LHAKAGEILVKETNVQRVESRVTICGDIHGQLYDFKELFSVGGKTP<ETNYLFMRDCMEHDF<LGIETFL

Parental  LLLALKVRYPDRITLIRGNHESRQITQVYGFYDECLRKYGSVTVWRYCTEI-FDYLSLSAIIDGKIFCVH
          LLL.L.V.Y.D.IT.I.GNH.S.QI.QVYGF..ECL..Y..VT.W.YC.E..FDY.SLSAII.G......
Retrocopy LLLVLNV*YNDHITKILGNH*SCQIPQVYGFFAECL*EYDLVTTWCYCPEL>FDYISLSAIINGNLLRAR

Parental  GGLSPSIQTLDQIRTIDRKQEVPHDG
          ..LSPSIQTLDQI...D.KQEVPH.G
Retrocopy -VLSPSIQTLDQIQMTD*KQEVPHEG

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	12.62 RPM
SRP017611_kidney	0.00 RPM	22.05 RPM
SRP017611_liver	0.00 RPM	10.51 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1043 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1043 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015223	1 retrocopy	retro_amel_286,
Canis familiaris	ENSCAFG00000017089	1 retrocopy	retro_cfam_16,
Ciona savignyi	ENSCSAVG00000004266	1 retrocopy	retro_csav_27,
Equus caballus	ENSECAG00000022179	1 retrocopy	retro_ecab_911,
Felis catus	ENSFCAG00000014171	1 retrocopy	retro_fcat_1043 ,
Felis catus	ENSFCAG00000025139	1 retrocopy	retro_fcat_1884,
Felis catus	ENSFCAG00000029685	1 retrocopy	retro_fcat_1086,
Macropus eugenii	ENSMEUG00000000397	5 retrocopies	retro_meug_1014, retro_meug_1188, retro_meug_1336, retro_meug_560, retro_meug_859,
Ornithorhynchus anatinus	ENSOANG00000008136	1 retrocopy	retro_oana_25,
Pan troglodytes	ENSPTRG00000007984	1 retrocopy	retro_ptro_28,
Tursiops truncatus	ENSTTRG00000005532	1 retrocopy	retro_ttru_1015,