RetrogeneDB ID:

retro_fcat_62

Retrocopy
location
Organism:Cat (Felis catus)
Coordinates:F1:7563443..7564772(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSFCAG00000013340
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:BECN1
Ensembl ID:ENSFCAG00000013136
Aliases:None
Description:beclin 1, autophagy related [Source:HGNC Symbol;Acc:1034]


Retrocopy-Parental alignment summary:






>retro_fcat_62
CTTAGAGTCAAAGTAAGAGCCTCCACCATGTTCCCCATCCGCTTCATTTGCCAGTGCTGCAAGCAGCCGCTAAAGCTGAA
TCAGTCCATGGAGACCTCAGGTCTTGAGACCACCCAAGAACCTACAGCTTCCACACTCTCAGCTCAGTGGGAGCCAGGAG
AAACCCTGGAAAGAGGCCCTGCCTCCAAGGCAGAGACAGATACTGAGAAGCTACAGGATAGTACCTCCTGCTCCACCCTC
CCTGGAGATGATGGCAAGATGTCCAGGGACAGTTCTAGCAACTTCATCTTACTTGGAGAGTTTGCCCCTACAAGTATGCT
CAGTAACGCCCAGAAGACTGCTGGGGACATTTTTGACATCCTGACTGGTGAAAGAGATGTGGACCACGCCCTGTGTGAGG
ACTGTACTGACAAACTTTTAGAGGAGCTGGACACCCAACTCATTCTCACAGAAACAGAGAACCAGAACTACAAACATTGG
AGGAAGAGAATACATGACGGGGAGCTGGAGACACTGCAGGAGGAGCTGGAGGGCCTGGAGCTGGAGGAAGCAAGGCTGGC
TCAAGAGCTGGAGGAGGTGGAGAAGAACCAAAAAAGAGTAGCAGAGGATCTTGAGGCAGCCCGAGCAGAGACTCAAGTGC
TGGACCAGCAGGATGAGCAGCACTGGAGGGACTACAGTAACTTACAATGGCAGCAACTGGAACTGCAGGATGAGCTGACC
AGCAGGAGGAACCAGCTGGTACGTGCCCAGATCCAGTGGGACTGGCTGAAGAAGACCAATGTCTTCAGTGCCACCTTTGA
GATCAGGGATGATGGCCCTGTGGGCATCATCAATAGCTTCAGATTGGGCTGCCTCCCCACTGTCCCCGTGAGCTGGAATG
AGATCAACATGGCCTGGGGACAGACAGCCTTGCTACTTCATGCCCTGTCCAACAAGATTGGGCTGGAGTTTCAGAGGTAT
CAACTCTTCCCCTGTGGAAACCGGTCCTATCTGAAGTCTTTAACAGATGACGCCATTGAGCTGCCATTGTTCTGCATCAC
AGGGCAGATTACTTGCTTGGATGTCAAATTTGACCTCGCAATGATGGCTTTTTTGGACTGCATGCAGCAGTTCCAGGAAG
AGGCTGAGAAAGGCAAGTGGGGTCTCTGCCTGCCCTGCAAGATTCATGTGGAAAATGGCCTGATGGAAGACTCTGGAAGC
ACTGGTGAGTTCTATTCCATCAGAACCTGCCTGAACACGGAGGAGCAGTGGACAAAGGCACTCAAGCTCGTGCTTATAAA
TTTTAAGTGTAGTCTTGCTTGGCTGTCTTTAAAATATTGTCAAAAATAA

ORF - retro_fcat_62 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 53.14 %
Parental protein coverage: 99.11 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKTSSSTM-QVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLATAQVKPGETQEEEANSGEEPFIETRQ
K...STM....F.CQ.C.QPLKL..S.......T.QE.TA..L..AQ..PGET.E....S..E...E..Q
RetrocopyKVRASTMFPIRFICQCCKQPLKLNQSMETSGLETTQEPTASTLS-AQWEPGETLERGPASKAETDTEKLQ
ParentalDGVSRRFIP-PARMMSTESANSFTLIGEASDGGTMENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTDTL
D..S....P.....MS..S...F.L.GE........N.....K..GD.FDI..G..DVDH.LCE.CTD.L
RetrocopyDSTSCSTLPGDDGKMSRDSSSNFILLGEFAPTSMLSNAQ---KTAGDIFDILTGERDVDHALCEDCTDKL
ParentalLDQLDTQLNVTENECQNYKRCLEILEQMNEDDSGQLQMELKELALEEERLIQELEDVEKNRKIVAENLEK
L..LDTQL..TE.E.QNYK................LQ.EL..L.LEE.RL.QELE.VEKN.K.VAE.LE.
RetrocopyLEELDTQLILTETENQNYKHWRK---RIHDGELETLQEELEGLELEEARLAQELEEVEKNQKRVAEDLEA
ParentalVQAEAERLDQEEAQYQREYSEFKRQQLELDDELKSVENQMRYAQMQLDKLKKTNVFNATFHIWHSGQFGT
..AE...LDQ...Q..R.YS....QQLEL.DEL.S..NQ...AQ.Q.D.LKKTNVF.ATF.I...G..G.
RetrocopyARAETQVLDQQDEQHWRDYSNLQWQQLELQDELTSRRNQLVRAQIQWDWLKKTNVFSATFEIRDDGPVGI
ParentalINNFRLGRLPSVPVEWNEINAAWGQTVLLLHALANKMGLKFQRYRLVPYGNHSYLESLTDKSKELPLYCS
IN.FRLG.LP.VPV.WNEIN.AWGQT.LLLHAL.NK.GL.FQRY.L.P.GN.SYL.SLTD...ELPL.C.
RetrocopyINSFRLGCLPTVPVSWNEINMAWGQTALLLHALSNKIGLEFQRYQLFPCGNRSYLKSLTDDAIELPLFCI
ParentalGGLRFFWDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRMDVEKGKIEDTGGSGGSYSIKTQFNSEEQ
.G.....D.KFD.AM.AFLDC.QQF.EE.EKG....CLP....VE.G..ED.G..G..YSI.T..N.EEQ
RetrocopyTGQITCLDVKFDLAMMAFLDCMQQFQEEAEKGKWGLCLPCKIHVENGLMEDSGSTGEFYSIRTCLNTEEQ
ParentalWTKALKFMLTNLKWGLAWVSSQFYNK
WTKALK..L.N.K..LAW.S.....K
RetrocopyWTKALKLVLINFKCSLAWLSLKYCQK

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 91 .59 RPM
SRP017611_kidney 0 .00 RPM 79 .05 RPM
SRP017611_liver 0 .00 RPM 25 .27 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_62 retrocopy.

TSS - click to see more details

Felis catus was not studied using FANTOM5 data.

Lab - click to see more details

retro_fcat_62 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 18 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000068671 retrocopy
retro_amel_16,
Bos taurus ENSBTAG000000199141 retrocopy
retro_btau_226,
Callithrix jacchus ENSCJAG000000131441 retrocopy
retro_cjac_330,
Dipodomys ordii ENSDORG000000009561 retrocopy
retro_dord_675,
Felis catus ENSFCAG00000013136 1 retrocopy
retro_fcat_62 ,
Homo sapiens ENSG000001265811 retrocopy
retro_hsap_335,
Macropus eugenii ENSMEUG000000117001 retrocopy
retro_meug_600,
Macaca mulatta ENSMMUG000000299711 retrocopy
retro_mmul_81,
Monodelphis domestica ENSMODG000000150641 retrocopy
retro_mdom_1778,
Mus musculus ENSMUSG000000350861 retrocopy
retro_mmus_390,
Nomascus leucogenys ENSNLEG000000118401 retrocopy
retro_nleu_1776,
Oryctolagus cuniculus ENSOCUG000000159643 retrocopies
retro_ocun_1021, retro_ocun_1732, retro_ocun_218,
Procavia capensis ENSPCAG000000140491 retrocopy
retro_pcap_345,
Pan troglodytes ENSPTRG000000228191 retrocopy
retro_ptro_268,
Sorex araneus ENSSARG000000003671 retrocopy
retro_sara_136,
Sus scrofa ENSSSCG000000173861 retrocopy
retro_sscr_75,
Ictidomys tridecemlineatus ENSSTOG000000126121 retrocopy
retro_itri_25,
Tursiops truncatus ENSTTRG000000117161 retrocopy
retro_ttru_595,


Copyright © RetrogeneDB 2014-2017