RetrogeneDB ID: retro_fcat_159

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:90741485..90741930(+)
• Located in intron of: ENSFCAG00000001881

Retrocopy information

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

Parental gene information

• Parental gene symbol: FIGLA
• Ensembl ID: ENSFCAG00000013444
• Aliases: None
• Description: folliculogenesis specific basic helix-loop-helix [Source:HGNC Symbol;Acc:24669]

Sequence

>retro_fcat_159
AGTTCAAGTGGTTACCTCCAACTGGTGCTGGAGCAGGAGCACGTGGCCAACACCAAAGAGTATGAGTGGATAAAAAATCT
GAACTTCGGTTTTGCCAAACTGAAGGCACTTGTGCTATTTCTTCCCCAGAGCAGGAAGCACAGCAAAGCTGATATCCTTA
AAGGTGCAACTGAATACATGTAAGTTCCCAGTGATATTTTCAAAAGAGCCAAAGACTCAGAAGAAAATCCAGATCACCAG
AACTATAGCAACAATACTTCTGAACCACATATATCCTTGGCTTGAAATCTATCGAGAAACAACACCCAATATGCCAGCTG
TATTGTGGGCTTGAAGAATGAGGAGGAAAGGCCCGGGGCAGATGGTAGCAGTGGTGAGTCAGCATACACTTAGTCGCCAG
AGCATGATGTCTAGGACTGGAGAGATCTCCCCAACCGGGAGTCTG

Alignment

ORF - retro_fcat_159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.19 %
• Parental protein coverage: 69.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSTEDLQLVLERRRVANAKERERYQKILNRGFAKLKALVPFLPQSRKPSKVDILKGATEYIQVLSDVLEG
          SS...LQLVLE...VAN.KE.E...K.LN.GFAKLKALV.FLPQSRK.SK.DILKGATEY..V.SD....
Retrocopy SSSGYLQLVLEQEHVANTKEYE-WIKNLNFGFAKLKALVLFLPQSRKHSKADILKGATEYM*VPSDIFKR

Parental  AKDSERQNLDHQSYSNNVSEPPISLARGLSRNITQHASCTVGLKNEEERPWADGGSGESAHT-CRQSMMS
          AKDSE..N.DHQ.YSNN.SEP.ISLA..LSRN.TQ.ASC.VGLKNEEERP.ADG.SGESA.T..RQSMMS
Retrocopy AKDSE-ENPDHQNYSNNTSEPHISLA*NLSRNNTQYASCIVGLKNEEERPGADGSSGESAYT>SRQSMMS

Parental  TTGVISPTRSL
          .TG.ISPT.SL
Retrocopy RTGEISPTGSL

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.10 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_159 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_159 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	ENSAMEG00000015931	1 retrocopy	retro_amel_1592,
Callithrix jacchus	ENSCJAG00000019358	1 retrocopy	retro_cjac_3644,
Felis catus	ENSFCAG00000013444	1 retrocopy	retro_fcat_159 ,