RetrogeneDB ID: retro_fcat_1925

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:64018392..64018928(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHTOP
• Ensembl ID: ENSFCAG00000002740
• Aliases: None
• Description: chromatin target of PRMT1 [Source:HGNC Symbol;Acc:24511]

Sequence

>retro_fcat_1925
CAGAAGACCTTAAATCAGCATCTGGATAAAAGTAATATCCAGGCATGGTTAGGTCGACATATAGGGGCCTTGGCCAGGGG
AGGAATTGGAGAACAAAGCCTGCCCATAATCCAGAGAGGCGTGCCCAGAGGAGGACTATGTGGGGGACTTGCCACAGAAC
CCTGCTTAGTGGGAGGGTGGGGGATGTCACTCTGAGGTTAAAACCTGCTCCAGGTGGGTGAGCTGTAGCTCCCCAAATGG
GTTTAAGAAGATGTGGTGTTCAAGGTCATGGAAGTCCTGGGAGAGGAGGCCTAGGGCATGGAGCTATGGGTCATGGTGAA
ATTGGTTATAGAGGTCAGGGTATGATGAGTTGGGGAAGAGGGAGCTTTGAATGCTGAGGTGGAGGCTGTGGGCCAGGGAG
AGGTACCCTCATTCACCCTGTACTGACCTGGGAGCAGCTGGACAACCAGTGGGATACATACATGTTGAAAATGAAAGGAC
ACCTGGATGCCAAGTTGGATGCCTACATGGCACAAAAAGATCCCAAAACCAATGAC

Alignment

ORF - retro_fcat_1925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.89 %
• Parental protein coverage: 71.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QKSLKQRLGKSNIQARLGRPIGTLARGAIGGRGLPIIQRGLPRGGLRGGRATRTLLRGG--MSLRGQNLL
          QK.L.Q.L.KSNIQA.LGR.IG.LARG.IG...LPIIQRG.PRGGL.GG.AT...L.GG..MSL.G.NLL
Retrocopy QKTLNQHLDKSNIQAWLGRHIGALARGGIGEQSLPIIQRGVPRGGLCGGLATEPCLVGGWGMSL*G*NLL

Parental  R-GGRAVAPRMGLRRGGVRGRGGPGRGGLGRGAMGRGGIGGRGRGMIGRGRGGFGGRGRGRGRGRGALTR
          ..GG.AVAP.MGLRR.GV.G.G.PGRGGLG.GAMG.G.IG.RG.GM...GRG.F...G.G.G.GRG.L..
Retrocopy Q<GG*AVAPQMGLRRCGVQGHGSPGRGGLGHGAMGHGEIGYRGQGMMSWGRGSFEC*GGGCGPGRGTLIH

Parental  PVLTKEQLDNQLDAYMSKTKGHLDAELDAYMAQTDPETND
          PVLT.EQLDNQ.D.YM.K.KGHLDA.LDAYMAQ.DP.TND
Retrocopy PVLTWEQLDNQWDTYMLKMKGHLDAKLDAYMAQKDPKTND

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	57.16 RPM
SRP017611_kidney	0.00 RPM	47.41 RPM
SRP017611_liver	0.00 RPM	40.64 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1925 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1925 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013518	1 retrocopy	retro_chof_6,
Callithrix jacchus	ENSCJAG00000010383	3 retrocopies	retro_cjac_2059, retro_cjac_423, retro_cjac_431,
Felis catus	ENSFCAG00000002740	1 retrocopy	retro_fcat_1925 ,
Myotis lucifugus	ENSMLUG00000016098	2 retrocopies	retro_mluc_201, retro_mluc_247,
Mus musculus	ENSMUSG00000001017	2 retrocopies	retro_mmus_1693, retro_mmus_1852,
Rattus norvegicus	ENSRNOG00000012760	1 retrocopy	retro_rnor_1095,
Ictidomys tridecemlineatus	ENSSTOG00000000660	1 retrocopy	retro_itri_1169,
Tupaia belangeri	ENSTBEG00000012442	1 retrocopy	retro_tbel_293,
Vicugna pacos	ENSVPAG00000010259	1 retrocopy	retro_vpac_353,