RetrogeneDB ID: retro_fcat_1673

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: E1:42067991..42068424(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRTAP4-1
• Ensembl ID: ENSFCAG00000005246
• Aliases: None
• Description: keratin associated protein 4-1 [Source:HGNC Symbol;Acc:18907]

Sequence

>retro_fcat_1673
TCTTGCTGCCAGCCTACGTGCTGCAGGACCACCTGCTGCCGGACCACCTGCTGCCAGCCCAGCGGCTGTGGGTCCAGCGG
CTGCGGACACAACTGCGGTGGGTCTAGCGGCTGTGGGTCCAGCTGCTGCCAGCCTTGCTGCTGCCCAACTTGCTGTCACA
CCACCTGCTGCCGGACCACCTGCTGCCAGCCCAGCTGCTGTGGGTCCAGCGGCTGTGGACAAAACTGCTGTGGGTCCCAC
TGCTGCCAGCCAGTTTGCTGTACCCCCGTGTACTGCACAAGAACCTGCTACCACCCCACCTGCTGCTGCCTGCCTGGGTG
CCTAGCCCAGGACTGTGGATCCAGCCACTGCTAGCCTGACTACTGCTCAATATGCTGTCAGTCCACTTGCTGTAGGACCA
CATGCTGCTGCCCTTGCTGTGTCCAGCTGCTGC

Alignment

ORF - retro_fcat_1673 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.09 %
• Parental protein coverage: 74.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TCCRPSCCQTTCCRTTCCRPSCCGSSCCRPCCGGSSCCGSSCCQPCCRPTCCQTTCCRTTCCRPSCCGSS
          .CC.P.CC.TTCCRTTCC.PS.CGSS.C...CGGSS.CGSSCCQPCC.PTCC.TTCCRTTCC.PSCCGSS
Retrocopy SCCQPTCCRTTCCRTTCCQPSGCGSSGCGHNCGGSSGCGSSCCQPCCCPTCCHTTCCRTTCCQPSCCGSS

Parental  CCRPSCCISSCCRPCCCRPSCCISSCCRPSCCQTACCRPSCCGSSCCGSSCCRPSCCISSCCRPSCCGSS
          .C...CC.S.CC.P.CC.P..C...C..P.CC....C.P.C.....CGSS.C.P..C.S.CC...CC...
Retrocopy GCGQNCCGSHCCQPVCCTPVYCTRTCYHPTCC----CLPGCLAQD-CGSSHC*PDYC-SICCQSTCCRTT

Parental  CCRPSC-CP-SCC
          CC.P.C.CP.SCC
Retrocopy CCCPCC<CP<SCC

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	0.11 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1673 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1673 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000005246	1 retrocopy	retro_fcat_1673 ,
Otolemur garnettii	ENSOGAG00000003102	1 retrocopy	retro_ogar_94,
Ictidomys tridecemlineatus	ENSSTOG00000004308	1 retrocopy	retro_itri_544,
Tupaia belangeri	ENSTBEG00000008312	1 retrocopy	retro_tbel_13,