RetrogeneDB ID:

retro_fcat_1590

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:D4:61939789..61941283(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSFCAG00000002741
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSFCAG00000022000
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_fcat_1590
TCTTCGGCAGCCGCCCTCCCCAGCCCCATCCTGAATCCAGACATCCGCTACAACCAGCTGTTCATCAACAATGAGTGGCA
AGATGCAGCCAGCAAGAAGACCTTCCCAACAGTGAACCCCACCACAGGAGAGGTCATTGGCCACGTGGCTGAAGGGGACC
GGGCTGATGTGGATCGGGCTGTGAAAGCAGCCCGTGAGGCCTTCCGCCTGGGGTCTCCGTGGCGCCGGATGGATGCTTCA
GAGCGGGGCCGGCTGCTGAACCGCCTGGCTGACCTTGTGGAGCGGGATCGTGTCTACCTGGCCTCACTGGAGACCTTGGA
CAACGGGAAGCCTTTCCAGGAGTCTTATGTCTTGGACCTGGATGAGGTCATCAAAGTATACCGGTACTTTGCCGGCTGGG
CCGACAAGTGGCACGGCAAGACCATCCCTATGGATGGCGAGCATTTCTGCTTCACCCGGCATGAGCCTGTTGGTGTCTGT
GGCCAGATAATCCCATGGAACTTCCCCTTGGTCATGCAGGGCTGGAAGCTTGCCCCAGCGCTTGCCACAGGCAACACTGT
GGTCATGAAGGTGGCAGAGCAGACCCCCCTTTCTGCCCTGTACTTGGCCTCCCTCATTAAAGAGGCGGGCTTTCCCCCTG
GGGTGGTGAACATCATCACTGGCTATGGCCCGACGGCAGGAGCGGCCATCGCCCAGCACATGGATATTGACAAAGTTGCC
TTCACCGGCTCCACTGAGGTGGGCCACCTGATCCAGAAGGCGGCTGGCGATTCCAACCTGAAGAGAGTCACCCTGGAGCT
GGGCGGGAAGAGCCCCAGCATCGTGTTGGCCGACGCTGACCTGGGCCATGCTGTGGAGCAGTGCCACGAAGCCCTATTCT
TCAACATGGGCCAGTGCTGCTGTGCAGGCTCCCGGACCTTCGTCGAAGAATCCATCTACGATGAGTTTCTCGAGAGAACC
GTGGAGAAGGCTAAGCAGAGAAGAGTCGGGAACCCCTTTGAACTGGACACTCAGCAGGGGCCCCAGGTGGACAAGGAGCA
ATTCGAACGAATCCTGAGCTATATCCGGCTTGGCCAGAAGGAGGGGGCAAAACTTCTCTGCGGTGGGGAGCGTTTGGGGG
AGCGTGGTTTCTTCATCAATCCCACGGTCTTTGGTGGTGTGCAGGATGACATGAGGATCGCCAGAGAGGAGATCTTTGGG
CCTGTGCAGCCCCTGTTTAAATTCAAGAAGATGGAGGAGGTGATCGAGAGGGCCAACAATACCAGATATGGCTTGGCTGC
CGCCGTGTTCACTCGGGACCTGGACAAAGCCATGTACTTCACACAGGCACTCCAGGCTGGCACAGTGTGGGTAAACACCT
ACAACATTGTCACCTGCCACACGCCATTTGGAGGGTTTAAGGAATCTGGCAATGGGAGGGAGCTGGGGGAGGATGGGCTA
AAGGCCTACACCGAGGTCAAGACAGTTACCATCAAGATTCCTCAGAAGAACTCA

ORF - retro_fcat_1590 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.9 %
Parental protein coverage: 96.32 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAATQAVPAPNQQPEVLFNQIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARDAFQW
....A.P.P...P....NQ.FINNEW.DA.S.KTFPTVNP.TGEVI..VAEGD..DVD.AVKAAR.AF..
RetrocopySSAAALPSPILNPDIRYNQLFINNEWQDAASKKTFPTVNPTTGEVIGHVAEGDRADVDRAVKAAREAFRL
ParentalGSPWRRMDASDRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK
GSPWRRMDAS.RGRLLNRLADL.ERDR.YLA.LETLDNGKP...SY..DLD.V.K..RY.AGWADK.HGK
RetrocopyGSPWRRMDASERGRLLNRLADLVERDRVYLASLETLDNGKPFQESYVLDLDEVIKVYRYFAGWADKWHGK
ParentalTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAG
TIP.DG..F..TRHEPVGVCGQIIPWNFPL.MQ.WKL.PALATGN.VVMKVAEQTPL.ALY.A.LIKEAG
RetrocopyTIPMDGEHFCFTRHEPVGVCGQIIPWNFPLVMQGWKLAPALATGNTVVMKVAEQTPLSALYLASLIKEAG
ParentalFPPGVVNIIPGFGPTAGAAIASHQDVDKVAFTGSTEVGHLIQIAAGSSNLKRVTLELGGKSPNIIMSDAD
FPPGVVNII.G.GPTAGAAIA.H.D.DKVAFTGSTEVGHLIQ.AAG.SNLKRVTLELGGKSP.I...DAD
RetrocopyFPPGVVNIITGYGPTAGAAIAQHMDIDKVAFTGSTEVGHLIQKAAGDSNLKRVTLELGGKSPSIVLADAD
ParentalMNWAVEQAHFALFFNQGQCCCAGSRTFVQEDVYAEFVERSVARAKSRVVGNPFDSQTEQGPQVDKTQFQK
...AVEQ.H.ALFFN.GQCCCAGSRTFV.E..Y.EF.ER.V..AK.R.VGNPF...T.QGPQVDK.QF..
RetrocopyLGHAVEQCHEALFFNMGQCCCAGSRTFVEESIYDEFLERTVEKAKQRRVGNPFELDTQQGPQVDKEQFER
ParentalVLGYIKSGKEEGAKLLCGGGAAADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVIGRANN
.L.YI..G..EGAKLLCGG.....RG.FI.PTVFG.VQD.M.IA.EEIFGPV....KFK..EEVI.RANN
RetrocopyILSYIRLGQKEGAKLLCGGERLGERGFFINPTVFGGVQDDMRIAREEIFGPVQPLFKFKKMEEVIERANN
ParentalSKYGLAAAVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGNGRELGEYGLQAYTEVKTVT
..YGLAAAVFT.DLDKA.Y..QALQAGTVWVN.Y.......PFGG.K.SGNGRELGE.GL.AYTEVKTVT
RetrocopyTRYGLAAAVFTRDLDKAMYFTQALQAGTVWVNTYNIVTCHTPFGGFKESGNGRELGEDGLKAYTEVKTVT
ParentalIKVPQKNS
IK.PQKNS
RetrocopyIKIPQKNS

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 .33 RPM 157 .93 RPM
SRP017611_kidney 2 .68 RPM 672 .04 RPM
SRP017611_liver 41 .85 RPM 562 .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_1590 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_1590 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 21 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000136641 retrocopy
retro_amel_51,
Bos taurus ENSBTAG000000087431 retrocopy
retro_btau_48,
Canis familiaris ENSCAFG000000086831 retrocopy
retro_cfam_1493,
Equus caballus ENSECAG000000176732 retrocopies
retro_ecab_1054, retro_ecab_1061,
Felis catus ENSFCAG00000022000 1 retrocopy
retro_fcat_1590 ,
Homo sapiens ENSG000001112751 retrocopy
retro_hsap_19,
Gorilla gorilla ENSGGOG000000071081 retrocopy
retro_ggor_33,
Latimeria chalumnae ENSLACG000000117981 retrocopy
retro_lcha_108,
Microcebus murinus ENSMICG000000034871 retrocopy
retro_mmur_19,
Myotis lucifugus ENSMLUG000000170841 retrocopy
retro_mluc_1918,
Macaca mulatta ENSMMUG000000083361 retrocopy
retro_mmul_247,
Mustela putorius furoENSMPUG000000022821 retrocopy
retro_mputfur_27,
Mus musculus ENSMUSG000000294551 retrocopy
retro_mmus_222,
Nomascus leucogenys ENSNLEG000000000161 retrocopy
retro_nleu_22,
Otolemur garnettii ENSOGAG000000330931 retrocopy
retro_ogar_203,
Pongo abelii ENSPPYG000000049661 retrocopy
retro_pabe_32,
Pteropus vampyrus ENSPVAG000000131891 retrocopy
retro_pvam_163,
Rattus norvegicus ENSRNOG000000013441 retrocopy
retro_rnor_307,
Sus scrofa ENSSSCG000000098891 retrocopy
retro_sscr_9,
Ictidomys tridecemlineatus ENSSTOG000000150091 retrocopy
retro_itri_33,
Xenopus tropicalis ENSXETG000000209301 retrocopy
retro_xtro_12,




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