RetrogeneDB ID: retro_fcat_1999

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:80697157..80697838(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISG20L2
• Ensembl ID: ENSFCAG00000006559
• Aliases: None
• Description: interferon stimulated exonuclease gene 20kDa-like 2 [Source:HGNC Symbol;Acc:25745]

Sequence

>retro_fcat_1999
GAGTTCCAGAGTGCCCTCCCAAAGATTATGAGCCACTCAACTTGCCTCTAGAAGTAAGGACCCCAGAAGAACCCTACTCA
GAAGAATGCTCTATGGAACTCTACCCAATCTCATTCAGAGAATAAATGCTCTGGAGCATCCTAGAAGATGCCAAAGAAGA
TGATGCCAATTGACTGTGAGATGGTGGGCACAGGATCCCAGGGGCATATAAGTTCTTTGGCCTGATGTAGCACTGTCAAC
TACCATGGAGATGTGCTTTATGATGAGTACATCCTTCCCCCCTGCCACATCGTGGACTACCGGACAAGATAGAGTGGCAT
CTGGAAGCAGTGCATGATGAATGATACACCCTTTAAGATTACTCAGAACCAGATCTTGAAGATACTCACAGGGAAGATAG
TGGTGGGGCATCCCATTCACAATTTCAAAGCCCTTTAGTACTTCCACACCACATCCCTCACCTGCAACACCTCCCATATC
CTCCCAGCCATCAAACGGAAGGTTGACTGCCTGGAGAATGCTACCATGTCTCTGAAGAATCTCACCAAGAAGCTTCTGAA
ATGGGACATCCAGATTGGGAAAAGTGGACATTCTTCTGTGGAAGACGCTCAAGTCACCATTAAGTTGTATGAGTTGGCTG
AAGTCGGGTGGGAACAGCCTGCCCCAGAATCCCCCAAAAGA

Alignment

ORF - retro_fcat_1999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.49 %
• Parental protein coverage: 65.23 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EFQSALPKTRSHPARSQKKGPQKNPTQKNAPQNSTQSHLENKCSGASQKTPGKMVAIDCEMVGTGPKGHV
          EFQSALPK..SH.....K.GPQKNPTQKNA..NSTQSH.ENKCSGAS.K.P.KM..IDCEMVGTG..GH.
Retrocopy EFQSALPKIMSHSTCL*K*GPQKNPTQKNALWNSTQSHSENKCSGAS*KMPKKMMPIDCEMVGTGSQGHI

Parental  SSLARCSIVNYHGDVLYDEYVLPPCHIVDYRTRWSGIRKQHMVNATPFKVARSQILKILAGKIVVGHAIH
          SSLA.CS.VNYHGDVLYDEY.LPPCHIVDYRTR.SGI.KQ.M.N.TPFK....QILKIL.GKIVVGH.IH
Retrocopy SSLA*CSTVNYHGDVLYDEYILPPCHIVDYRTR*SGIWKQCMMNDTPFKITQNQILKILTGKIVVGHPIH

Parental  NDFKALQYSHPKSLTRDTSHI-PPLNRKAECPENATVSLKCLTKKLLNRDIQVGKSGHSSVEDAQATMEL
          N.FKAL.Y.H..SLT..TSHI.P...RK..C.ENAT.SLK.LTKKLL..DIQ.GKSGHSSVEDAQ.T..L
Retrocopy N-FKAL*YFHTTSLTCNTSHILPAIKRKVDCLENATMSLKNLTKKLLKWDIQIGKSGHSSVEDAQVTIKL

Parental  YKLVEVEWEQHLAQNPPK
          Y.L.EV.WEQ.....P..
Retrocopy YELAEVGWEQPAPESPKR

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	14.92 RPM
SRP017611_kidney	0.00 RPM	11.75 RPM
SRP017611_liver	0.00 RPM	7.58 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1999 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1999 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000006559	1 retrocopy	retro_fcat_1999 ,
Macaca mulatta	ENSMMUG00000000037	1 retrocopy	retro_mmul_1519,
Nomascus leucogenys	ENSNLEG00000012742	1 retrocopy	retro_nleu_3048,
Rattus norvegicus	ENSRNOG00000011402	2 retrocopies	retro_rnor_2836, retro_rnor_463,