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


Retrocopy-Parental alignment summary:






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

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:

ParentalKLHFRVWSHQTLKSDVLLGTAALDIFETLKSNNMKLEEVVVTLQLVGDKEPTETMGDLSVCLDGLQLEPE
KLHFRVWSHQTLKSDVLLGTAALDIFETLKSNNMKLE.VVVTLQLVG.KEPTET..D.SVCLDGLQLE.E
RetrocopyKLHFRVWSHQTLKSDVLLGTAALDIFETLKSNNMKLEKVVVTLQLVGYKEPTETIRDFSVCLDGLQLESE
ParentalVVTNGETTCSESASQNDDGSRPKDEARTNPNGSDEPEDSGAGENRKVNGNNSPSLSNGGFKPSRPPRPSR
VVTNGETTCSE..SQ..D.SRPKDEA.T.PNGSDEPEDSG.GENRKVNGNNSPSLSNGGFKPSRPPRPS.
RetrocopyVVTNGETTCSECVSQTTDVSRPKDEAKTHPNGSDEPEDSGTGENRKVNGNNSPSLSNGGFKPSRPPRPS*
ParentalPPPPTPRRPASVNGSPSATSESDGSSTGSLPPTNINSNTSEGATSGLIIPLTISGGSGPRPLNTVPQAPL
PPP.TP.RP.SVNGSPSATSE.DGSS.GSLPPTNIN.NTSEGAT.GLIIPL.ISGGSGPRPLN.VPQ.PL
RetrocopyPPPLTPCRPVSVNGSPSATSENDGSSMGSLPPTNIN*NTSEGATPGLIIPLNISGGSGPRPLNPVPQDPL
ParentalPPGWEQRVDQHGRVYYVDHIEKRTTWDRPEPLPPGWERRVDNMGRIYYVDHFTRTTTWQRPTLESVRNYE
P.GWEQRV.QHGRVYY.D.IE.RT.W.RPEPLPPGWE..VDNMG.IYYVD.FTRTTTWQRPT.ES....E
RetrocopyPSGWEQRVVQHGRVYYIDLIERRTMWNRPEPLPPGWEQWVDNMGHIYYVDNFTRTTTWQRPTVESIQDGE
ParentalQWQLQRSQLQGAMQQFNQRFIYGNQDLFTTSQNKEFDPLGPLPPGWEKRTDSNGRVYFVNHNTRITQWED
QWQLQ.SQLQGAMQQFNQRF.YGNQDLFTTSQNKEFDPL..LPPGWEKRTD.NGRVYFVNHN..ITQWED
RetrocopyQWQLQCSQLQGAMQQFNQRFTYGNQDLFTTSQNKEFDPLLSLPPGWEKRTDGNGRVYFVNHNSCITQWED
ParentalPRSQGQLNEKPLPEGWEMRFTVDGIPYFVDHNRRTTTYIDPRTGKSALDNGPQIAYVRDFKAKVQYFRFW
PRSQG.LNEK.LPEGWEMRFTVDGIPYFVDHNRRTTTYIDPRTGKSALDN.P.IAYVRDFKA.VQYFRFW
RetrocopyPRSQGKLNEKLLPEGWEMRFTVDGIPYFVDHNRRTTTYIDPRTGKSALDNRPPIAYVRDFKANVQYFRFW
ParentalCQQLAMPQHIKITVTRKTLFEDSFQQIMSFNPQDLRRRLWVIFPGEEGLDYGGVAREWFFLLSHEVLNPM
CQQLAMPQHIKIT.TRKTLFEDS.QQIMSFNPQDLRRRLWVIFPG.EGLDYGGVARE.FF.LS..VLNPM
RetrocopyCQQLAMPQHIKITGTRKTLFEDSLQQIMSFNPQDLRRRLWVIFPGKEGLDYGGVARERFFVLSNKVLNPM
ParentalYCLFEYAGKDNYCLQINPASYINPDHLKYFRFIGRFIAMALFHGKFIDTGF
YC.FEYAGKDNYCLQINPASYINPDHLKYF.FI.R.IAMA.FHGKFIDTGF
RetrocopyYCPFEYAGKDNYCLQINPASYINPDHLKYFCFIDRLIAMASFHGKFIDTGF

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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 - click to see more details

Felis catus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_fcat_899 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_899 was not experimentally validated.

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.
Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000003081 retrocopy
retro_btau_1692,
Choloepus hoffmanni ENSCHOG000000111151 retrocopy
retro_chof_2100,
Felis catus ENSFCAG00000008780 1 retrocopy
retro_fcat_899 ,




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