RetrogeneDB ID:

retro_fcat_116

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:X:73971667..73972816(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSFCAG00000004998
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSFCAG00000015254
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_fcat_116
ATGGGGAGTGGAGAGCCTAATCCTGCTGGCAAGAAAAAGAAGTACCTCAAGGCTGCCCTGTACGTGGGTGACTTGGACCC
AGATGTTACTGAGGACATGTTATATAAAAAGTTCAGGCCTGCTGGCCCTCTGCGCTTCACCCGAATCTGCCGTGACCCTG
TGACCCGCAGCCCCCTGGGCTATGGCTATGTTAACTTCCGCTTTCCTGCAGATGCTGAGTGGGCCCTGAATACCATGAAT
TTTGATTTGATTAATGGCAAACCTTTCCGCCTCATGTGGTCTCAGCCAGATGACCGCTTAAGAAAGTCTGGAGTTGGAAA
TATATTCATCAAAAACCTGGACAAATCCATAGATAATAGGGCCCTTTTTTATTTATTTTCTGCTTTTGGGAACATTCTCT
CCTGCAAAGTCGTATGTGATGACAATGGCTCTAAGGGTTATGCCTATGTGCACTTTGACAGCCTGGCCGCTGCCAATAGA
GCCATCTGGCATATGAATGGGGTGCGGCTCAACAACCGCCAGGTGTATGTTGGTAGATTCAAATTCCCAGAAGAGAGGGC
AGCTGAAGTCAGAACCAAGGATAGAGCAACTTTCACTAATGTTTTTGTTAAAAACTTCGGAGATGACATGGATGATGAAA
AACTGAAGGAAATCTTTAGTGGATATGGGCCAACTGAGAGTGTTAAGGTAATAAGAGATGCTAGTGGGAAATCTAAGGGC
TTTGGATTTGTGAGGTATGAGACGCACGAGGCTGCCCAAAAGGCTGTGTTAGACCTGCATGGAAAGTCCATCAATGGGAA
AGTTCTGTACGTAGGGCGAGCACAGAAGAAAATTGAACGATTGGCTGAGTTAAGACGAAGATTTGAACGGCTGAGATTAA
AAGAAAAAAGTCGGCCTCCGGGGGTGCCTATCTATATTAAGAACCTGGATGAGACCATCGATGATGAAAAACTGAAGGAA
GAATTTTCTTCCTTTGGATCAATTAGCCGGGCCAAAGTGATGGTGGAAGTAGGGCAAGGCAAAGGGTTTGGTGTTGTCTG
CTTCTCCTCTTTTGAAGATGCTACCAAAGCAGTGGATGAGATGAATGGTCGCACAGTGGGCTCCAAGCCCCTGCATGTCA
CCCTGGGCCAGGCCAGGCGCAGGTGGTGA

ORF - retro_fcat_116 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.4 %
Parental protein coverage: 55.15 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI
Y..A.LYVGDL..DVTE.MLY.KF.PAGP....R.CRD..TR..LGY.YVNF..PADAE.AL.TMNFD.I
RetrocopyYLKAALYVGDLDPDVTEDMLYKKFRPAGPLRFTRICRDPVTRSPLGYGYVNFRFPADAEWALNTMNFDLI
ParentalKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYAFVHFET
.GKP.R.MWSQ.D..LRKSGVGN.FIKNLDKSIDN.AL...FSAFGNILSCKVVCD.NGSKGYA.VHF..
RetrocopyNGKPFRLMWSQPDDRLRKSGVGNIFIKNLDKSIDNRALFYLFSAFGNILSCKVVCDDNGSKGYAYVHFDS
ParentalQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAK-EFTNVYIKNFGEEVDDESLKELFSQFGK
..AA..AI..MNG..LN.R.V.VGRFK...ER.AE...K....FTNV..KNFG...DDE.LKE.FS..G.
RetrocopyLAAANRAIWHMNGVRLNNRQVYVGRFKFPEERAAEVRTKDRATFTNVFVKNFGDDMDDEKLKEIFSGYGP
ParentalTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGRAQKKVERQAELKRKFEQLKQE
T.SVKV.RD.SGKSKGFGFV.YE.HE.A.KAV....GK.I.GKV..VGRAQKK.ER.AEL.R.FE.L...
RetrocopyTESVKVIRDASGKSKGFGFVRYETHEAAQKAVLDLHGKSINGKVLYVGRAQKKIERLAELRRRFERLRLK
ParentalRISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMNGR
..SR..GV..YIKNLD.TIDDEKL..EFS.FGSI..AKVM.E.G..KGFG.VCFSS.E.ATKAV.EMNGR
RetrocopyEKSRPPGVPIYIKNLDETIDDEKLKEEFSSFGSISRAKVMVEVGQGKGFGVVCFSSFEDATKAVDEMNGR
ParentalIVGSKPLYVALAQRK
.VGSKPL.V.L.Q..
RetrocopyTVGSKPLHVTLGQAR

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 2 .64 RPM 35 .46 RPM
SRP017611_kidney 0 .52 RPM 52 .25 RPM
SRP017611_liver 0 .30 RPM 53 .88 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_116 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_116 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 28 parental genes, and 62 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000115352 retrocopies
retro_amel_107, retro_amel_676,
Bos taurus ENSBTAG000000171253 retrocopies
retro_btau_1492, retro_btau_28, retro_btau_656,
Canis familiaris ENSCAFG000000030812 retrocopies
retro_cfam_45, retro_cfam_837,
Choloepus hoffmanni ENSCHOG000000053273 retrocopies
retro_chof_1150, retro_chof_1182, retro_chof_1274,
Callithrix jacchus ENSCJAG000000025123 retrocopies
retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Cavia porcellus ENSCPOG000000095522 retrocopies
retro_cpor_1330, retro_cpor_77,
Equus caballus ENSECAG000000093962 retrocopies
retro_ecab_2, retro_ecab_502,
Felis catus ENSFCAG000000018741 retrocopy
retro_fcat_1927,
Felis catus ENSFCAG00000015254 2 retrocopies
retro_fcat_116 , retro_fcat_545,
Homo sapiens ENSG000000906212 retrocopies
retro_hsap_109, retro_hsap_74,
Gorilla gorilla ENSGGOG000000040023 retrocopies
retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Loxodonta africana ENSLAFG000000001513 retrocopies
retro_lafr_1144, retro_lafr_390, retro_lafr_597,
Microcebus murinus ENSMICG000000166331 retrocopy
retro_mmur_675,
Myotis lucifugus ENSMLUG000000120682 retrocopies
retro_mluc_228, retro_mluc_397,
Macaca mulatta ENSMMUG000000074971 retrocopy
retro_mmul_178,
Monodelphis domestica ENSMODG000000176572 retrocopies
retro_mdom_1090, retro_mdom_1805,
Mustela putorius furoENSMPUG000000144142 retrocopies
retro_mputfur_152, retro_mputfur_546,
Mus musculus ENSMUSG000000112577 retrocopies
retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Nomascus leucogenys ENSNLEG000000119282 retrocopies
retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus ENSOCUG000000005622 retrocopies
retro_ocun_153, retro_ocun_792,
Otolemur garnettii ENSOGAG000000040671 retrocopy
retro_ogar_71,
Ochotona princeps ENSOPRG000000119841 retrocopy
retro_opri_1133,
Pongo abelii ENSPPYG000000015062 retrocopies
retro_pabe_190, retro_pabe_2563,
Pan troglodytes ENSPTRG000000005733 retrocopies
retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Rattus norvegicus ENSRNOG000000156422 retrocopies
retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii ENSSHAG000000181391 retrocopy
retro_shar_823,
Sus scrofa ENSSSCG000000036603 retrocopies
retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Tursiops truncatus ENSTTRG000000143402 retrocopies
retro_ttru_1117, retro_ttru_246,


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