RetrogeneDB ID: retro_fcat_483

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A3:76096334..76096817(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPAP2C
• Ensembl ID: ENSFCAG00000024319
• Aliases: None
• Description: phosphatidic acid phosphatase type 2C [Source:HGNC Symbol;Acc:9230]

Sequence

>retro_fcat_483
GCCTCTTTGCCTTTTGCCATCCTGACTCTTGTGAACGCCCCATATAAGCACGGCCTCTACTGCAGAGAAGACTCCATCCA
GTACCCCTACTGTCCAGACACCATCACCCATGAGTTCATGGCCAGAGGTCACCATCACAGCCACCATCATCCTTGTCTCA
ACCAAGGAGGCCTGCCTGGTGCACACAGACTGCCTCTATTCCCATTCCAACTTCAACAACAGAGTGGCTGGCTTCTATAA
GGTGCTGAGAAAGTTCCTGTTCAGGGCTGCAATGAGTCAGTCACTGGCAGACCTGGCCAAGGTCACGATAGGCCATCTGT
GGCCCAACTTCCTGGCTAAGTGTGACCCTGACTTGAGCCACTTCAACTGCTCTGTCTACCTGCATGTGGAGAAGATGTGC
AGGGAAAGCCTAGTAACATCACCGAGTCCAGAATGTCTTTCTACTCCGGACACTCCTCCTTTGGGATGTTTGTGGTGCTC
TAT

Alignment

ORF - retro_fcat_483 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.78 %
• Parental protein coverage: 55.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ASLPFAILTLVNAPYKRGFYCGDDSIRYPYRPDTITHGLMAG-VTITATIILVSAGEAYLVYTDRLYSRS
          ASLPFAILTLVNAPYK.G.YC..DSI.YPY.PDTITH..MA..VTITATIILVS..EA.LV.TD.LYS.S
Retrocopy ASLPFAILTLVNAPYKHGLYCREDSIQYPYCPDTITHEFMAR>VTITATIILVSTKEACLVHTDCLYSHS

Parental  DFNNYVAAVYKVLGTFLFGAAVSQSLTDLAKYMIGRLRPNFLAVCDPDWSRVNCSVYVQVEKVCR-GSPA
          .FNN.VA..YKVL..FLF.AA.SQSL.DLAK..IG.L.PNFLA.CDPD.S..NCSVY..VEK.CR.G.P.
Retrocopy NFNNRVAGFYKVLRKFLFRAAMSQSLADLAKVTIGHLWPNFLAKCDPDLSHFNCSVYLHVEKMCR<GKPS

Parental  NVTESRLSFYSGHSSFGMYCMMF
          N.TESR.SFYSGHSSFGM.....
Retrocopy NITESRMSFYSGHSSFGMFVVLY

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	7.92 RPM
SRP017611_kidney	0.00 RPM	31.23 RPM
SRP017611_liver	0.00 RPM	3.84 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_483 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_483 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019734	1 retrocopy	retro_cfam_397,
Felis catus	ENSFCAG00000024319	1 retrocopy	retro_fcat_483 ,
Ictidomys tridecemlineatus	ENSSTOG00000019777	2 retrocopies	retro_itri_1139, retro_itri_1721,