RetrogeneDB ID: retro_fcat_1263

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:44687097..44687861(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000023835
• Aliases: None
• Description: None

Sequence

>retro_fcat_1263
CCCCAGTCCCAGTTGCAGGAGATCTCATTTGCCTCAACCCTGAAAGAGGTTCTTGACAACCTAGACAGTCACCTGAAGAA
ATCTGAATACTTTTGCTTTCCTCTGGTTCCCACACCGTGAGAAGATCAGTGTCATCCACCAGGACCACACCAACAAGCCT
CCCTCCTCTTCAGCCAACTGGTTTTGGAACTATGTTATCAGATTCTCTTTACTAGAGTTCTTGCTCTGGATCAGTGCCTT
CCTGCAGGGTCCTGTGGGATGGATAAATCACCCCCTTTTGGCTCCTGTTCACGTGGAAGAAGGAGGGAAGCAACCTCGGC
CATAAGATCTTCACCTATGAGTGCCTCTCAAAGCAGCATGTCCAGGATAGGGTCATCCCCAGACAGAAGACCAAAGAGGC
CTTGCTAGAACTGAAGGTCATTGTGGGAGCCCACCCCAAGATGGTGGCCTACTGCCCTGTGGAGGTGTGCTTCATCCAGG
GGATGACATCCTGTTGAGTTCTTCCTTCCAGAGGCACAGCTGCTACATGAATATCATTATGTACGAGTTATATGCAAGGA
TGTGCCATGGCTGGACTACTGACTGGCTTAGGAGACCATCATGAAGACAGTCCAGGTCCGGCTCCCCCTTGGTCAAGGCC
CACAGCTGTATGTTGAAGGACTTTTGAGAAAATCTATCTAGCCTTTTCGAAGTTCTGTGTCATTTGAGAAAAGCTAAACC
CCACTAGGATATTTCTAAATGCATATCTGAAGAAAGTATTGTAC

Alignment

ORF - retro_fcat_1263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.73 %
• Parental protein coverage: 57.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  PQFHLQEISFPSTLDEVLDNLDSHLKKSEYF-RFLWFPHSENVSVIYQDHTNKPPSSSANWFWDYAIGFY
          PQ..LQEISF.STL.EVLDNLDSHLKKSEYF..FLWFPH.E..SVI.QDHTNKPPSSSANWFW.Y.I.F.
Retrocopy PQSQLQEISFASTLKEVLDNLDSHLKKSEYF>AFLWFPHREKISVIHQDHTNKPPSSSANWFWNYVIRFS

Parental  LLEFLLWISSFLPGLVGWINR-FFFWLLFTRKRESSNLSHEIFTYECRFKQHVQDWAIPREKTKEALLEL
          LLEFLLWIS.FL.G.VGWIN...F..L....K.E.SNL.H.IFTYEC..KQHVQD..IPR.KTKEALLEL
Retrocopy LLEFLLWISAFLQGPVGWINH>PFWLLFTWKK-EGSNLGHKIFTYECLSKQHVQDRVIPRQKTKEALLEL

Parental  KAVLETHPKMVAHFPVEVRFTR-GDDILLSPCFQRDSCYMNIIMYRPYG-KDIPRLDYWLAYETIMKKVG
          K.....HPKMVA..PVEV.F...GDDILLS..FQR.SCYMNIIMY..Y..KD.P.LDY.LA.ETIMK.V.
Retrocopy KVIVGAHPKMVAYCPVEVCFIQ<GDDILLSSSFQRHSCYMNIIMYELYA<KDVPWLDY*LA*ETIMKTVQ

Parental  GR-PHWAKMHACMCRD-FEKMYPAFSKFCAIREKLDPTGMFLNAYLEKVFY
          .R.....K.H.CM..D.FEK.Y.AFSKFC.I.EKL.PT..FLNAYL.KV.Y
Retrocopy VR>SPLVKAHSCMLKD>FEKIYLAFSKFCVI*EKLNPTRIFLNAYLKKVLY

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	0.23 RPM
SRP017611_kidney	0.00 RPM	0.31 RPM
SRP017611_liver	0.00 RPM	67.02 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1263 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1263 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000147	1 retrocopy	retro_amel_895,
Canis familiaris	ENSCAFG00000008414	1 retrocopy	retro_cfam_1517,
Felis catus	ENSFCAG00000023835	1 retrocopy	retro_fcat_1263 ,