RetrogeneDB ID: retro_fcat_899

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B3:61941493..61943116(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ITCH
• Ensembl ID: ENSFCAG00000008780
• Aliases: None
• Description: itchy E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:13890]

Sequence

>retro_fcat_899
AAATTACATTTTCGTGTGTGGAGTCATCAGACACTGAAATCTGATGTTTTGTTGGGAACTGCTGCATTAGATATCTTTGA
AACCTTAAAGTCAAACAACATGAAACTTGAGAAAGTAGTTGTGACTTTACAGCTTGTAGGTTACAAAGAGCCAACAGAGA
CAATAAGAGACTTTTCAGTTTGTCTTGATGGGCTGCAGTTAGAGTCTGAAGTTGTTACCAATGGTGAAACTACATGTTCA
GAATGTGTTTCACAGACTACTGATGTCTCCAGACCCAAGGATGAAGCAAAAACACATCCAAATGGATCAGATGAACCTGA
GGATTCAGGGACTGGTGAAAATAGGAAGGTCAATGGGAATAATTCTCCATCACTCTCAAATGGCGGTTTTAAACCTTCTA
GGCCTCCCAGACCTTCATGACCACCTCCACTTACCCCATGTAGACCAGTATCTGTCAATGGTTCACCATCTGCCACTTCT
GAAAATGATGGATCCAGTATGGGCTCTCTGCCACCAACAAATATAAATTGAAATACATCTGAAGGAGCAACACCTGGATT
AATAATTCCTCTTAATATATCTGGAGGCTCAGGCCCTAGGCCACTAAATCCTGTACCTCAAGATCCCCTACCATCTGGCT
GGGAGCAGAGAGTGGTCCAGCATGGGCGAGTTTACTACATAGATCTTATTGAAAGAAGAACAATGTGGAATAGACCAGAA
CCTCTACCTCCTGGCTGGGAACAGTGGGTTGACAACATGGGACATATTTATTATGTTGACAATTTCACAAGAACAACAAC
ATGGCAGAGGCCAACAGTGGAATCCATCCAGGACGGTGAACAGTGGCAGCTCCAATGTAGTCAGCTTCAAGGAGCAATGC
AGCAGTTTAACCAGAGATTCACTTATGGGAATCAGGATTTGTTTACTACATCGCAAAATAAAGAATTTGATCCCCTTCTT
TCCCTGCCTCCTGGATGGGAGAAGAGAACAGACGGCAATGGTAGAGTATATTTCGTCAACCACAACTCTTGTATTACACA
ATGGGAGGACCCCAGAAGTCAAGGTAAATTAAATGAAAAGCTCTTACCTGAAGGCTGGGAAATGAGATTCACAGTAGATG
GAATTCCATATTTTGTGGACCACAATAGAAGAACGACCACCTATATTGACCCCCGCACTGGAAAATCTGCTCTAGACAAT
AGACCACCGATAGCCTATGTACGGGACTTCAAGGCAAATGTTCAGTATTTCCGGTTCTGGTGTCAGCAACTTGCGATGCC
ACAGCATATAAAGATTACAGGGACAAGAAAAACGTTGTTTGAAGATTCCTTGCAGCAGATAATGAGCTTCAATCCCCAAG
ATCTGCGAAGACGTTTGTGGGTGATTTTTCCAGGAAAAGAAGGTTTAGATTATGGAGGTGTAGCAAGAGAGAGGTTCTTT
GTTTTGTCAAACAAGGTGTTGAACCCCATGTATTGCCCGTTTGAATATGCAGGGAAGGATAACTACTGCTTGCAGATTAA
TCCTGCTTCTTACATCAATCCAGATCACCTGAAATATTTTTGTTTTATAGATAGGCTTATTGCCATGGCTTCGTTCCATG
GGAAATTCATAGACACAGGTTTT

Alignment

ORF - retro_fcat_899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.99 %
• Parental protein coverage: 62.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLHFRVWSHQTLKSDVLLGTAALDIFETLKSNNMKLEEVVVTLQLVGDKEPTETMGDLSVCLDGLQLEPE
          KLHFRVWSHQTLKSDVLLGTAALDIFETLKSNNMKLE.VVVTLQLVG.KEPTET..D.SVCLDGLQLE.E
Retrocopy KLHFRVWSHQTLKSDVLLGTAALDIFETLKSNNMKLEKVVVTLQLVGYKEPTETIRDFSVCLDGLQLESE

Parental  VVTNGETTCSESASQNDDGSRPKDEARTNPNGSDEPEDSGAGENRKVNGNNSPSLSNGGFKPSRPPRPSR
          VVTNGETTCSE..SQ..D.SRPKDEA.T.PNGSDEPEDSG.GENRKVNGNNSPSLSNGGFKPSRPPRPS.
Retrocopy VVTNGETTCSECVSQTTDVSRPKDEAKTHPNGSDEPEDSGTGENRKVNGNNSPSLSNGGFKPSRPPRPS*

Parental  PPPPTPRRPASVNGSPSATSESDGSSTGSLPPTNINSNTSEGATSGLIIPLTISGGSGPRPLNTVPQAPL
          PPP.TP.RP.SVNGSPSATSE.DGSS.GSLPPTNIN.NTSEGAT.GLIIPL.ISGGSGPRPLN.VPQ.PL
Retrocopy PPPLTPCRPVSVNGSPSATSENDGSSMGSLPPTNIN*NTSEGATPGLIIPLNISGGSGPRPLNPVPQDPL

Parental  PPGWEQRVDQHGRVYYVDHIEKRTTWDRPEPLPPGWERRVDNMGRIYYVDHFTRTTTWQRPTLESVRNYE
          P.GWEQRV.QHGRVYY.D.IE.RT.W.RPEPLPPGWE..VDNMG.IYYVD.FTRTTTWQRPT.ES....E
Retrocopy PSGWEQRVVQHGRVYYIDLIERRTMWNRPEPLPPGWEQWVDNMGHIYYVDNFTRTTTWQRPTVESIQDGE

Parental  QWQLQRSQLQGAMQQFNQRFIYGNQDLFTTSQNKEFDPLGPLPPGWEKRTDSNGRVYFVNHNTRITQWED
          QWQLQ.SQLQGAMQQFNQRF.YGNQDLFTTSQNKEFDPL..LPPGWEKRTD.NGRVYFVNHN..ITQWED
Retrocopy QWQLQCSQLQGAMQQFNQRFTYGNQDLFTTSQNKEFDPLLSLPPGWEKRTDGNGRVYFVNHNSCITQWED

Parental  PRSQGQLNEKPLPEGWEMRFTVDGIPYFVDHNRRTTTYIDPRTGKSALDNGPQIAYVRDFKAKVQYFRFW
          PRSQG.LNEK.LPEGWEMRFTVDGIPYFVDHNRRTTTYIDPRTGKSALDN.P.IAYVRDFKA.VQYFRFW
Retrocopy PRSQGKLNEKLLPEGWEMRFTVDGIPYFVDHNRRTTTYIDPRTGKSALDNRPPIAYVRDFKANVQYFRFW

Parental  CQQLAMPQHIKITVTRKTLFEDSFQQIMSFNPQDLRRRLWVIFPGEEGLDYGGVAREWFFLLSHEVLNPM
          CQQLAMPQHIKIT.TRKTLFEDS.QQIMSFNPQDLRRRLWVIFPG.EGLDYGGVARE.FF.LS..VLNPM
Retrocopy CQQLAMPQHIKITGTRKTLFEDSLQQIMSFNPQDLRRRLWVIFPGKEGLDYGGVARERFFVLSNKVLNPM

Parental  YCLFEYAGKDNYCLQINPASYINPDHLKYFRFIGRFIAMALFHGKFIDTGF
          YC.FEYAGKDNYCLQINPASYINPDHLKYF.FI.R.IAMA.FHGKFIDTGF
Retrocopy YCPFEYAGKDNYCLQINPASYINPDHLKYFCFIDRLIAMASFHGKFIDTGF

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	41.78 RPM
SRP017611_kidney	0.00 RPM	24.94 RPM
SRP017611_liver	0.00 RPM	24.97 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_899 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_899 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000308	1 retrocopy	retro_btau_1692,
Choloepus hoffmanni	ENSCHOG00000011115	1 retrocopy	retro_chof_2100,
Felis catus	ENSFCAG00000008780	1 retrocopy	retro_fcat_899 ,