RetrogeneDB ID:

retro_fcat_820

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:B3:27207750..27209234(+)
Located in intron of:ENSFCAG00000000153
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ARNT
Ensembl ID:ENSFCAG00000003644
Aliases:None
Description:aryl hydrocarbon receptor nuclear translocator [Source:HGNC Symbol;Acc:700]


Retrocopy-Parental alignment summary:






>retro_fcat_820
ACAGGGCGTATCCTTCCAGACCTGAAGACTGGAACAATGAAAAAGGAAGGCCAACAGTCTTCCATGAAGATGTGTATGGG
CTCAAGGAGATAATTTATTTGCCGTAGAAGGTGCAGCAATAGCTCTGTGGACCCAGTCTCCATGAATAGACTGAGCTTTG
TGAGGAACAGATGCAGGAATGGACTTGGCTCTGTGAAGAATGGGGAACCTCATTTTGTGGTGGTCCACTGCACAGGCTAT
ATCAAGGCCTGGCCCCCAGCAGGTGTCTTCCTCCCAGATGATGATCCAGAGGCTGGCCAGGGGAGCAAATTTTGCCTAGT
GGCCATTGGCAGACTACAGGTAACCAGTTCTCCCAACTGTACAGACATGAGTAACATTTGTCGACCGACAGAGTTCATCT
CACGGCACAACATTGAGGGGATATTCACTTTTGTGGAACACCGCTGTGTGGCTACTGTTGGCTACCAACCACAGGAACTC
TTAGGAAAGAATATTGTAGAATTCTCTCATCCTGAAGACCAACAGCTTCTAAGAGACAGCTTGTAACAAGTGGTGAAGTT
AAAAGGCCAAGTGTTGTCTGTCATGTTCCGGTTCTGGTCTAAGAACCGGGAATGGCTCTGGATGAGAACCAGCTCCTTTA
CTTTCCAGAACACTTACTCAGATGAAATTGAGTACATCATCTGTACCACCAATGTGAAGAACTCCAGCCATCAACCAAGG
CCTACACTGTCCAACACAATCCAGAGACCACAGGTAGGTCCCATGGCTAATTTACCCTTAGAGATGGGCTCAGGGCAGTT
GGCATCCAGGAAGCATCAACAGCAAACAGAATTGGATGTGGTATCAGGAAACAATGGACTGGCTGGCTACAATCATTCCC
AGGTTTCTGTTCAGCCTGTAACAACCACAGGGCCAGAACACAGTAAGCCCCTTGAGAAGTCAGATGGTCTGTTTGCCAAG
GATAGAGATCCAAGATTTTCAGAAATCTACTCCAACATCAGTGCAGATCAGAGTAAAGGCATCTCCTCCAGCACTGTCCC
TGCCATCCAACAGCTATTCTCACAGGACAACACATTCCCTCCTACCCCCACCCCCGGCCGGCAGAGAATTTCAGAAATAG
TGATCTGGCCTCTCCTGTAACCATCGTCCAGCCATCAGCTTCTGCAGGGTAGATGTTGGCCCAGATTTCCCACCACTCCA
ACTCACCCCCAAGGAACCCCAACTTGGACCCTACCACCCGCCCAGACTTCTCTGCCCAGCAGGTGGCTACTCAGGCTACA
GCCAAGACTCGTTCTTCCCAGTTTGGTATGGGAAGCTTTCAGACTCCGTCCTCCTTCAGCCCCATGTCCCTCCCTGGTGC
TTCAACTGCGTCACCTGGTGCTGCTGCCTCCCCTAGTCTCACCAATCATGGATCCAACTTTGCTCCTGAGACTGGACAGA
CTACAGGACAATTCCAGACACAGACAGCAGAGGGTGTAAGTCTG

ORF - retro_fcat_820 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.6 %
Parental protein coverage: 60.1 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalSGRIL-DLKTGTVKKEGQQSSMRMCMGSRRSFICRMRCGNSSVDPVSMNRLSFVRNRCRNGLGSVKDGEP
.GRIL.DLKTGT.KKEGQQSSM.MCMGSRR.FICR.RC.NSSVDPVSMNRLSFVRNRCRNGLGSVK.GEP
RetrocopyTGRILPDLKTGTMKKEGQQSSMKMCMGSRR*FICRRRCSNSSVDPVSMNRLSFVRNRCRNGLGSVKNGEP
ParentalHFVVVHCTGYIKAWPPAGVSLPDDDPEAGQGSKFCLVAIGRLQVTSSPNCTDMSNVCQPTEFISRHNIEG
HFVVVHCTGYIKAWPPAGV.LPDDDPEAGQGSKFCLVAIGRLQVTSSPNCTDMSN.C.PTEFISRHNIEG
RetrocopyHFVVVHCTGYIKAWPPAGVFLPDDDPEAGQGSKFCLVAIGRLQVTSSPNCTDMSNICRPTEFISRHNIEG
ParentalIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKNREWLWMRT
IFTFV.HRCVATVGYQPQELLGKNIVEF.HPEDQQLLRDS..QVVKLKGQVLSVMFRF.SKNREWLWMRT
RetrocopyIFTFVEHRCVATVGYQPQELLGKNIVEFSHPEDQQLLRDSL*QVVKLKGQVLSVMFRFWSKNREWLWMRT
ParentalSSFTFQNPYSDEIEYIICTNTNVKNSSQEPRPTLSNTIQRPQLGPTANLPLEMGSGQLASRQQQQQTELD
SSFTFQN.YSDEIEYIICT.TNVKNSS..PRPTLSNTIQRPQ.GP.ANLPLEMGSGQLASR..QQQTELD
RetrocopySSFTFQNTYSDEIEYIICT-TNVKNSSHQPRPTLSNTIQRPQVGPMANLPLEMGSGQLASRKHQQQTELD
ParentalVVSGRDGLTGYNHSQVSVQPVTTTGPEHSKPLEKSDSLFAQDRDPRFSEIYSNISADQSKGISSSTVPAT
VVSG..GL.GYNHSQVSVQPVTTTGPEHSKPLEKSD.LFA.DRDPRFSEIYSNISADQSKGISSSTVPA.
RetrocopyVVSGNNGLAGYNHSQVSVQPVTTTGPEHSKPLEKSDGLFAKDRDPRFSEIYSNISADQSKGISSSTVPAI
ParentalQQLFSQ-GNTFP--PTPRPAENFRNSGLASPVTIVQPSASAGQMLAQISRHSNPP-QGAAPTWT-PSTRP
QQLFSQ.G...P..P.PRPAENFRNS.LASPVTIVQPSASAG.MLAQIS.HSN.P.QG..PTWT.P.TRP
RetrocopyQQLFSQ<GQHIPSYPHPRPAENFRNSDLASPVTIVQPSASAG*MLAQISHHSNSP>QGT-PTWT<PTTRP
ParentalGFSAQQVATQATAKTRSSQFGVGSFQTPSSFSPMSLPGASTASPGAAAYPSLTNRGSNFAPETGQTTGQF
.FSAQQVATQATAKTRSSQFG.GSFQTPSSFSPMSLPGASTASPGAAA.PSLTN.GSNFAPETGQTTGQF
RetrocopyDFSAQQVATQATAKTRSSQFGMGSFQTPSSFSPMSLPGASTASPGAAASPSLTNHGSNFAPETGQTTGQF
ParentalQTRTAEGVSV
QT.TAEGVS.
RetrocopyQTQTAEGVSL

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 .11 RPM 29 .96 RPM
SRP017611_kidney 0 .00 RPM 18 .24 RPM
SRP017611_liver 0 .00 RPM 18 .60 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_820 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_820 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Felis catus ENSFCAG00000003644 1 retrocopy
retro_fcat_820 ,


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