RetrogeneDB ID: retro_fcat_1023

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:36788485..36788846(-)
• Located in intron of: ENSFCAG00000014340

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORAOV1
• Ensembl ID: ENSFCAG00000026606
• Aliases: None
• Description: oral cancer overexpressed 1 [Source:HGNC Symbol;Acc:17589]

Sequence

>retro_fcat_1023
AGGTTTCCTGGAGGAGGGTTTCAGAAAGGCTATGAAGAAGGCAATAGTGTAGGTATAAATGAAGGAAGACAATATGGCAC
ATTACATGGAGTTAAAAATCAGCTCTGAGATGGAGTGCTACCAAGTGTTGCTTTTGCTTGGCAATGTCTCCTCCACAGTT
ATGCCACTGAGAAAGACAGCAAAAGGATGAAAGTTTTAGAATCATTGACTGGAATGATTCACAAATTCCCTTATGATGAT
CCTACTTACAATAAACTTAATAAAGACTTAGACAAAAATAAAAGGTAAATGTAAACAGCTTTGTTCATTATTGAATGTTT
AGTGGGACTTTACAATTAGTGTGAAAGGTTCTGGACTTTCA

Alignment

ORF - retro_fcat_1023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.85 %
• Parental protein coverage: 99.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RFHGEGYQEGYEEGSSLGIIEGRRYGTLHGA-KIGSELVSYD-SIPFPFPLKVHECATEKDSKKMKALES
          RF.G.G.Q.GYEEG.S.GI.EGR.YGTLHG..KI.SE...Y..S..F......H..ATEKDSK.MK.LES
Retrocopy RFPGGGFQKGYEEGNSVGINEGRQYGTLHGV>KISSEMECYQ<SVAFAWQCLLHSYATEKDSKRMKVLES

Parental  LIGMIQKFPYDDPTYDKLHEDLD-RIRGKFKQLCSLLNVQPDFKISAEGSGLS
          L.GMI.KFPYDDPTY.KL..DLD..I.GK.KQLCSLLNV..DF.IS..GSGLS
Retrocopy LTGMIHKFPYDDPTYNKLNKDLD>KIKGKCKQLCSLLNV*WDFTISVKGSGLS

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	44.65 RPM
SRP017611_kidney	0.00 RPM	27.83 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_1023 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1023 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001983	1 retrocopy	retro_amel_309,
Felis catus	ENSFCAG00000026606	1 retrocopy	retro_fcat_1023 ,
Homo sapiens	ENSG00000149716	1 retrocopy	retro_hsap_3131,
Microcebus murinus	ENSMICG00000003061	1 retrocopy	retro_mmur_410,
Tursiops truncatus	ENSTTRG00000017307	6 retrocopies	retro_ttru_1122, retro_ttru_1249, retro_ttru_1408, retro_ttru_1785, retro_ttru_272, retro_ttru_860,