RetrogeneDB ID: retro_fcat_1831

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F2:803102..803430(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUSC2
• Ensembl ID: ENSFCAG00000031595
• Aliases: None
• Description: tumor suppressor candidate 2 [Source:HGNC Symbol;Acc:17034]

Sequence

>retro_fcat_1831
CTGGGCACCGGCGGCTCCAAAGCCCGGGGGCCTGAGGCCCCTCGCCTCGGCGGCCGGGGGTGGAGGGCGGAGCCCCGGGG
TCGGCAGTCGCTGAGCAAGCTTTGGTGCGGCCGCGAGGCCGCGTCCGATCCCCCTTCGCATTTAGGCGCCACGGCTCCAA
GTTCTGCGATGAGGAAGGGGAACGGCTCACGAGGAGACAGTCGTCACCAGGAACGGGCAGAAGCGGGCCAAGCCGAGGCG
GGTACCTAAGAACCTGCTTCCTCAGGGCCTCGTGAAGCTGGATCCTCCCCGCGTCCACGTGGATTTTCCTGGGATCCTCT
ATGAGGTG

Alignment

ORF - retro_fcat_1831 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.57 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGASGSKAR-GLWPF--ASGAGG-GGPESAVAEQALVRPRGRVVPPFVFTRRGSMFYDEDGD-LAHEFYE
          .G..GSKAR.GL.P...A.G.GG.G.P.SAVAEQALVRPRGRV..PF.F.R.GS.F.DE.G...AHE...
Retrocopy LGTGGSKAR>GLRPLASAAGGGG>GAPGSAVAEQALVRPRGRVRSPFAFRRHGSKFCDEEGE<TAHE---

Parental  ETIVTKNGQKRAKLRRVHKNLIPQGIVKLDPPRIHVDFPVILYEV
          ET.VT.NGQKRAK.RRV.KNL.PQG.VKLDPPR.HVDFP.ILYEV
Retrocopy ETVVTRNGQKRAKPRRVPKNLLPQGLVKLDPPRVHVDFPGILYEV

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	6.20 RPM
SRP017611_kidney	0.00 RPM	2.27 RPM
SRP017611_liver	0.00 RPM	0.91 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1831 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1831 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000007859	2 retrocopies	retro_dord_20, retro_dord_590,
Felis catus	ENSFCAG00000031595	1 retrocopy	retro_fcat_1831 ,
Myotis lucifugus	ENSMLUG00000002499	1 retrocopy	retro_mluc_874,
Otolemur garnettii	ENSOGAG00000008080	3 retrocopies	retro_ogar_2293, retro_ogar_2714, retro_ogar_3421,
Tarsius syrichta	ENSTSYG00000010483	2 retrocopies	retro_tsyr_1922, retro_tsyr_2132,
Vicugna pacos	ENSVPAG00000007903	1 retrocopy	retro_vpac_221,