RetrogeneDB ID: retro_fcat_183

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:140533496..140533946(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSPH
• Ensembl ID: ENSFCAG00000021883
• Aliases: None
• Description: phosphoserine phosphatase [Source:HGNC Symbol;Acc:9577]

Sequence

>retro_fcat_183
GAGTTGAGGAAGCTTTTCTGTTCAGCTGATGCAGTATGCTTTGATGTTGATGGCACAGTTATCAGAGAAGAAGGAATTGA
TGAGCTAGCCAGATTCTGTGGAGGTGAGGATGCTGTGTCAGAAATGATCTGGAGAGCCGTGGGTGGGGCAGTGCCTTTCA
AGGCTGACCTCACAGAGCGCTTAGCTCTGGTCCAGCCCTCCAGGGAACAGGTGCAAAGGCTCATGGTAGAGCACCCCCCA
CGCCTGACCCCTGGCATAAAGGAGCTAGTAAGTCACCCGCAAGAGTGAAATGTTCAGCTTTTCTTAATATATGGTAGCTT
TAGGAGCATTGTAGACCATGTTGCTTCAAGGCTCAATATCCCATTAACCATTGTATTTGCTAATAGGCTGAAATTCTAGT
TTAATGGTGAATGTGCAGGTTTTGATGAGATGCAACCAACAGCCCAATCT

Alignment

ORF - retro_fcat_183 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.67 %
• Parental protein coverage: 54.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLRKLFCSADAVCFDVDSTVIREEGIDELAKFCGVEDAVSEMTRRAMGGAVPFKAALTERLALIQPSREQ
          .LRKLFCSADAVCFDVD.TVIREEGIDELA.FCG.EDAVSEM..RA.GGAVPFKA.LTERLAL.QPSREQ
Retrocopy ELRKLFCSADAVCFDVDGTVIREEGIDELARFCGGEDAVSEMIWRAVGGAVPFKADLTERLALVQPSREQ

Parental  VQRLIAEHPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPSTNVFANRLKFYFNGEYAG
          VQRL..EHPP.LTPGI.ELVS..QE.NVQ.FLI.G.FRSIV.HVAS.LNIP.T.VFANRLKF.FNGE.AG
Retrocopy VQRLMVEHPPRLTPGIKELVSHPQE*NVQLFLIYGSFRSIVDHVASRLNIPLTIVFANRLKF*FNGECAG

Parental  FDEMQPTAES
          FDEMQPTA.S
Retrocopy FDEMQPTAQS

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	8.03 RPM
SRP017611_kidney	0.00 RPM	23.08 RPM
SRP017611_liver	0.00 RPM	1.01 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_183 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_183 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016118	1 retrocopy	retro_amel_607,
Felis catus	ENSFCAG00000021883	1 retrocopy	retro_fcat_183 ,
Ictidomys tridecemlineatus	ENSSTOG00000026898	1 retrocopy	retro_itri_1159,