RetrogeneDB ID: retro_fcat_426

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A3:55336551..55337068(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF3A
• Ensembl ID: ENSFCAG00000006982
• Aliases: None
• Description: general transcription factor IIIA [Source:HGNC Symbol;Acc:4662]

Sequence

>retro_fcat_426
GTGTGTCCAACAGAATGCTCCTTTGTGGCAAAAACGTGGATAGAGCTTCTAAAACATGCGAGAGAAACCCATAAAGAGGA
CAGAAAATGCAAAGTATGCCAGAAAGCACATGAACACAAACATTCCCATAAGCAATATATGAAAACCCAGGCCCCAGAAA
GGAACTCATGCAGCTGCCAAGAGAGCCCTGTGAGTCAACCTGTGCACTGCTGCGTCTCATCTGCAGGGCCACACTCTCTC
TTCTCAGGAGGAAAGGCACGCGCTTGAGGGTGAACCAGGCAGCTGTGGCTAAACGTTTAGGATGGAACAGAGTCTCACTG
GGCATGCTGTTGTGCGTGGCCATGGCAAGAAGAAAATGAAGCTCAAAGTAAAACCTTCCCTTGAAAAATGGGGTTTGGCC
CCTCGTCTCAGTGGATATAATCCTCCTAACACAAAACAAGAACAAGATTTATCCTCGCCTGAACGTGGTGCGTCACTGAA
CTGTCCTGAAAACAAGGTGCCCTGGACGGTTGTGATA

Alignment

ORF - retro_fcat_426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.07 %
• Parental protein coverage: 53.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VCKKECSFVAKTWTELLKHMREAHKEAVRCEVCQKTFKRKDYLKQHMKTHAPEREVCRCPREGCGRTY-T
          VC..ECSFVAKTW.ELLKH.RE.HKE...C.VCQK....K...KQ.MKT.APER..C.C..........T
Retrocopy VCPTECSFVAKTWIELLKHARETHKEDRKCKVCQKAHEHKHSHKQYMKTQAPERNSCSCQESPVSQPV>T

Parental  TVFNLQSHILSFHEERRPFTCEHAGCGKTFAMKQSLTRHAVVHDPDKKKMNLKVKPSREKRSLASRLSGY
          ....LQ.H.LS..EER.....E...CG.TF.M.QSLT.HAVV....KKKM.LKVKPS.EK..LA.RLSGY
Retrocopy AASHLQGHTLSSQEERHALEGEPGSCG*TFRMEQSLTGHAVVRGHGKKKMKLKVKPSLEKWGLAPRLSGY

Parental  IPPKKKQGQSSSLPTNGESLNCTEGGVLSTVAI
          .PP..KQ.Q..S.P..G.SLNC.E..V..TV.I
Retrocopy NPPNTKQEQDLSSPERGASLNCPENKVPWTVVI

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	19.86 RPM
SRP017611_kidney	0.00 RPM	24.12 RPM
SRP017611_liver	0.00 RPM	24.56 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_426 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_426 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019373	1 retrocopy	retro_cjac_3066,
Equus caballus	ENSECAG00000014803	1 retrocopy	retro_ecab_866,
Felis catus	ENSFCAG00000006982	1 retrocopy	retro_fcat_426 ,
Gasterosteus aculeatus	ENSGACG00000003107	1 retrocopy	retro_gacu_6,
Gorilla gorilla	ENSGGOG00000008407	1 retrocopy	retro_ggor_2622,
Microcebus murinus	ENSMICG00000014763	1 retrocopy	retro_mmur_368,
Macaca mulatta	ENSMMUG00000009029	1 retrocopy	retro_mmul_1632,
Nomascus leucogenys	ENSNLEG00000000331	2 retrocopies	retro_nleu_1134, retro_nleu_214,
Oreochromis niloticus	ENSONIG00000014134	1 retrocopy	retro_onil_8,
Vicugna pacos	ENSVPAG00000004995	1 retrocopy	retro_vpac_456,