RetrogeneDB ID:

retro_fcat_1116

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:C1:118367815..118368838(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSFCAG00000008734
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TMEM185A
Ensembl ID:ENSFCAG00000024483
Aliases:LOC101093254, TMEM185A
Description:transmembrane protein 185A [Source:HGNC Symbol;Acc:17125]


Retrocopy-Parental alignment summary:






>retro_fcat_1116
TTCAACCCGAGTAAGTTCCTCATCTACGCCTGCCTGCTGCTCTTCTCCGTGCTGCTGCCCCTCCGCCTGGACGGCGTCAT
CCAGTGGAGCTACTGGGCGGTCTTCGCCCCCATATGGCTGTGGAAGCTCCTGGTCATCGCCGGCGCCTCAGTGGGCGCAG
GCGTTTGGGCCCGCAACCCTCGATACCGCACGGAGGGGGAGGCCTGCGTGGAGTTCAAAGCCATGTTGATCGCCGTGGCT
ATCCACCTGCTGCTGCTCATGTTCGAAGTCCTGGTCTGCGACAGGGTGGAGAGGGGGACCCACTTCTGGCTGCTGGTCTT
CATGCCACTTTTTTTCGTATCCCCAGTGTCCGTGGCCGCCTGCGTCTGGGGCTTCCGACACGATAGGTCCCTAGAGCTGG
AGATCTTGTGCTCTGTCAACATCCTGCAGTTCATCTTCATCGCCCTAAGGCTGGACAGGATTATCCACTGGCCGTGGCTG
GTGGTGTTCGTGCCCCTGTGGATTCTCATGTCGTTCCTCTGCCTAGTCGTCCTCTATTACATCGTCTGGTCCCTCCTGTT
CCTTCGATCCTTGGATGTCGTTGCGGAACAGCGAAGGACACATGTGACCATGGCCATCAGCTGGATAACGATTGTCGTGC
CCCTGCTCACTTTTGAGGTTCTGCTCGTTCACAGATTGGACGGCCACAATACATTCTCTTACATCTCCATATTTGTCCCC
CTTTGGCTTTCATTAATAACTTTAATGGCCACGACGTTTAGGCGGAAGGGAGGCAACCATTGGTGGTTTGGGATTCGCAG
AGATTTCTGTCAGTTTCTGCTTGAAATTTTCCCATTTCTAAGAGAATATGGGAACATTTCCTATGATCTACATCATGAAG
ATAGTGAAGAAGCTGAAGAAACATCAGTCCCAGATGCTCCTAAAATTGCTCCGATGTTTGGAAAGAAGGCCAGGGTAGTT
ATAACCCAGAGTCCTGGAAAGTATGTTCCCCCGCCTCCCAAGTTAAATATTGATATGCCAGAT

ORF - retro_fcat_1116 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.15 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalFSPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFAPIWLWKLMVIVGASVGTGVWARNPQYRAEGETCV
F.PSKFLIYACLLLFSVLL.LRLDG.IQWSYWAVFAPIWLWKL.VI.GASVG.GVWARNP.YR.EGE.CV
RetrocopyFNPSKFLIYACLLLFSVLLPLRLDGVIQWSYWAVFAPIWLWKLLVIAGASVGAGVWARNPRYRTEGEACV
ParentalEFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSVN
EFKAMLIAV.IHLLLLMFEVLVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSVN
RetrocopyEFKAMLIAVAIHLLLLMFEVLVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSVN
ParentalILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTHITMALSWMT
ILQFIFIALRLD.IIHWPWLVV.VPLWILMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH.TMA.SW.T
RetrocopyILQFIFIALRLDRIIHWPWLVVFVPLWILMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTHVTMAISWIT
ParentalIVVPLLTFEILLVHKLDGHNAFSCIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQFLLEIFPFL
IVVPLLTFE.LLVH.LDGHN.FS.I.IFVPLWLSLITLMATTF..KGGNHWWFGIR.DFCQFLLEIFPFL
RetrocopyIVVPLLTFEVLLVHRLDGHNTFSYISIFVPLWLSLITLMATTFRRKGGNHWWFGIRRDFCQFLLEIFPFL
ParentalREYGNISYDLHHEDTEETEETPVPEPPKIAPMFRKKTRVVITQSPGKYVLPPPKLNIEMPD
REYGNISYDLHHED.EE.EET.VP..PKIAPMF.KK.RVVITQSPGKYV.PPPKLNI.MPD
RetrocopyREYGNISYDLHHEDSEEAEETSVPDAPKIAPMFGKKARVVITQSPGKYVPPPPKLNIDMPD

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 3 .56 RPM 58 .30 RPM
SRP017611_kidney 3 .71 RPM 17 .62 RPM
SRP017611_liver 4 .04 RPM 9 .20 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_1116 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_1116 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 22 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000086371 retrocopy
retro_acar_65,
Ailuropoda melanoleuca ENSAMEG000000093511 retrocopy
retro_amel_8,
Bos taurus ENSBTAG000000068181 retrocopy
retro_btau_1,
Canis familiaris ENSCAFG000000191031 retrocopy
retro_cfam_159,
Dasypus novemcinctus ENSDNOG000000118641 retrocopy
retro_dnov_2451,
Dipodomys ordii ENSDORG000000150271 retrocopy
retro_dord_67,
Equus caballus ENSECAG000000093991 retrocopy
retro_ecab_426,
Felis catus ENSFCAG00000024483 1 retrocopy
retro_fcat_1116 ,
Homo sapiens ENSG000001559841 retrocopy
retro_hsap_104,
Gorilla gorilla ENSGGOG000000242681 retrocopy
retro_ggor_189,
Loxodonta africana ENSLAFG000000030441 retrocopy
retro_lafr_898,
Microcebus murinus ENSMICG000000046391 retrocopy
retro_mmur_106,
Macaca mulatta ENSMMUG000000028881 retrocopy
retro_mmul_310,
Mustela putorius furoENSMPUG000000118961 retrocopy
retro_mputfur_46,
Mus musculus ENSMUSG000000731391 retrocopy
retro_mmus_358,
Nomascus leucogenys ENSNLEG000000134871 retrocopy
retro_nleu_2723,
Otolemur garnettii ENSOGAG000000164141 retrocopy
retro_ogar_88,
Procavia capensis ENSPCAG000000091601 retrocopy
retro_pcap_260,
Pongo abelii ENSPPYG000000208091 retrocopy
retro_pabe_118,
Pteropus vampyrus ENSPVAG000000138221 retrocopy
retro_pvam_30,
Rattus norvegicus ENSRNOG000000110471 retrocopy
retro_rnor_6,
Tursiops truncatus ENSTTRG000000006431 retrocopy
retro_ttru_868,


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