RetrogeneDB ID: retro_fcat_1782

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F1:31502326..31502578(-)
• Located in intron of: ENSFCAG00000025437

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOLT1B
• Ensembl ID: ENSFCAG00000028655
• Aliases: None
• Description: golgi transport 1B [Source:HGNC Symbol;Acc:20175]

Sequence

>retro_fcat_1782
TTCAGAGTCTTCTTCCAAAAACATAACATGAAAGCTACAGGATTTTTCCTGGGTGGTATATTTGTTGTCCTTGTTGGTTG
GCCCTTCGGTAGGCATGATCTTTGAAATTTATTGATTTTGTTTCTTGTTTTCAGGGGCTTCTTTCCTATGGTCACTGGCT
TTATTAGAAGAGTGCCAGTCCCTGGGTTCCTCTTGAATTTACATGGAATTAGATCATTTGTTGATAAAGTTGGAGAAAGC
AACAATATGGTA

Alignment

ORF - retro_fcat_1782 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.4 %
• Parental protein coverage: 65.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FRFFFQKHKMKATGFFLGGVFVVLIGWPL-IGMIFEIYGF-FL-LFRGFFPVVIGFIRRVPVLGSLLNLP
          FR.FFQKH.MKATGFFLGG.FVVL.GWP...GMIFEIY.F.FL..FRGFFP.V.GFIRRVPV.G.LLNL.
Retrocopy FRVFFQKHNMKATGFFLGGIFVVLVGWPF>VGMIFEIY*FCFL<VFRGFFPMVTGFIRRVPVPGFLLNLH

Parental  GIRSFVDKVGESNNMV
          GIRSFVDKVGESNNMV
Retrocopy GIRSFVDKVGESNNMV

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	22.50 RPM
SRP017611_kidney	0.10 RPM	14.12 RPM
SRP017611_liver	0.10 RPM	5.16 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1782 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1782 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016231	1 retrocopy	retro_amel_604,
Canis familiaris	ENSCAFG00000012256	1 retrocopy	retro_cfam_1835,
Dasypus novemcinctus	ENSDNOG00000013576	2 retrocopies	retro_dnov_158, retro_dnov_1730,
Felis catus	ENSFCAG00000028655	1 retrocopy	retro_fcat_1782 ,
Oryctolagus cuniculus	ENSOCUG00000008797	1 retrocopy	retro_ocun_1706,
Otolemur garnettii	ENSOGAG00000004756	1 retrocopy	retro_ogar_3234,
Ictidomys tridecemlineatus	ENSSTOG00000006352	1 retrocopy	retro_itri_1786,