RetrogeneDB ID: retro_fcat_1800

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F2:15388575..15388912(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000022895
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDCD6
• Ensembl ID: ENSFCAG00000025521
• Aliases: None
• Description: programmed cell death 6 [Source:HGNC Symbol;Acc:8765]

Sequence

>retro_fcat_1800
CAGAGGGTTGACAAAGATAGGAGCCAACTGATACTGGACAATGAACTTCAGCAAGCACTATCCAATGGCACATGGACTCC
ACTGAATTCAGTGACTGTCAGGTCAATGATATCTCTGTTTGACCAAGAGAACAAGGCTGGTGTGACCTTCAGCGAATTCA
CTGTTATCTGGAAATACATCACAGACTGGCAGAATGTCTTCCACACTTACGGACAGGGACCACTCTAGGATGGTTGACAA
GAAAGAGCTCAAGCAAGCACTTTCAGTGTATGGGCCCTCTGACCAGTTTCACGACATCTTCATCCACAAGCGTGACATAC
AAGTATGGGGGCCCTTG

Alignment

ORF - retro_fcat_1800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.91 %
• Parental protein coverage: 60.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QRVDKDRSGVISDNELQQALSNGTWTPFNPVTVRSIISMFDRENKAGVNFSEFTGVWKYITDWQNVFRTY
          QRVDKDRS..I.DNELQQALSNGTWTP.N.VTVRS.IS.FD.ENKAGV.FSEFT..WKYITDWQNVF.TY
Retrocopy QRVDKDRSQLILDNELQQALSNGTWTPLNSVTVRSMISLFDQENKAGVTFSEFTVIWKYITDWQNVFHTY

Parental  -DRDNSGMIDKNELKQALSGFGYRLSDQFHDILIRKFDRQGRGQI
          .DRD.S.M.DK.ELKQALS..G...SDQFHDI.I.K.D.Q..G..
Retrocopy >DRDHSRMVDKKELKQALSVYG--PSDQFHDIFIHKRDIQVWGPL

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	24.68 RPM
SRP017611_kidney	0.10 RPM	36.28 RPM
SRP017611_liver	0.00 RPM	13.44 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1800 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1800 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008464	1 retrocopy	retro_amel_498,
Canis familiaris	ENSCAFG00000011044	2 retrocopies	retro_cfam_1289, retro_cfam_1695,
Felis catus	ENSFCAG00000025521	1 retrocopy	retro_fcat_1800 ,
Rattus norvegicus	ENSRNOG00000014485	1 retrocopy	retro_rnor_2840,