RetrogeneDB ID:

retro_rnor_154

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:5:111299566..111301420(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000006335
Aliases:Klhl9, RGD1304814
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Klhl13
Ensembl ID:ENSRNOG00000014029
Aliases:None
Description:Protein Klhl13 [Source:UniProtKB/TrEMBL;Acc:F1LM50]


Retrocopy-Parental alignment summary:






>retro_rnor_154
ATGAAGGTGTCGCTCGGTAACGGCGAGATGGGCGTCTCTGCCCACCTGCAGCCTTGCAAGGCTGGAACTACGCGGTTTTT
TACCAGCAATACGCACAGTTCTGTTGTATTGCAAGGCTTTGATCAGCTCAGAATAGAGGGACTGCTTTGTGACGTGACTC
TGGTACCAGGCGATGGAGAGGAAATCTTCCCAGTTCATAGAGCCATGATGGCGTCTGCCAGTGATTATTTCAAGGCCATG
TTCACAGGAGGAATGAAGGAGAAAGATCTAATGTGCATTAAGCTTCATGGGGTGAACAAAGTTGGTCTGAAGAAAATCAT
TGATTTTATTTATACTGCAAAACTCTCTCTCAATATGGACAATCTTCAGGATACTCTTGAGGCTGCCAGCTTTCTACAGA
TCTTGCCGGTTTTGGATTTTTGTAAAGTATTTCTTATATCTGGTGTCTCCTTAGATAACTGTGTTGAGGTTGGACGGATT
GCTAACACCTACAATCTTATAGAAGTGGATAAATACGTAAATAATTTCATCCTGAAGAACTTTCCTGCCTTGTTGAGTAC
CGGGGAGTTTCTAAAACTCCCCTTTGAACGGCTTGCCTTTGTGCTTTCCAGCAATAGTCTCAAGCACTGTTCTGAACTTG
AACTCTTCAAGGCAGCCTGCCGCTGGTTGAGGCTGGAAGACCCTCGGATGGACTATGCTGCAAAATTAATGAAGAATATT
CGCTTCCCACTGATGACGCCACAGGATCTCATCAACTATGTGCAGACAGTAGATTTCATGAGAACTGACAATACCTGTGT
GAATTTACTTTTGGAAGCAAGCAATTACCAAATGATGCCATATATGCAGCCAGTGATGCAGTCAGACAGAACTGCCATTC
GATCAGATTCTACTCATTTGGTTACGTTAGGAGGAGTTTTGAGGCAACAGCTGGTTGTAAGTAAAGAGTTACGGATGTAC
GACGAAAGGGCGCAGGAGTGGAAATCGTTAGCCCCTATGGATGCTCCTCGATACCAGCACGGCATTGCTGTTATTGGAAA
CTTCCTTTATGTAGTTGGTGGTCAGAGTAATTATGACACAAAAGGAAAAACTGCTGTTGATACAGTCTTCAGATTTGATC
CTCGTTATAATAAGTGGATGCAGGTGGCATCATTAAACGAAAAGCGCACATTTTTTCACCTGAGTGCACTCAAAGGACAT
TTATATGCAGTTGGTGGACGCAGTGCAGCTGGTGAACTGGCCACAGTAGAATGTTACAACCCAAGAATGAATGAATGGAG
CTATGTTGCAAAAATGAGTGAACCCCACTATGGCCATGCTGGAACAGTATATGGGGGTTTAATGTATATATCCGGAGGAA
TTACCCATGACACTTTCCAAAATGAGCTCATGTGTTTTGACCCAGATACAGACAAATGGACACAGAAGGCTCCTATGACT
ACAGTCCGAGGTCTGCATTGCATGTGTACAGTTGGAGACAAGCTGTATGTCATTGGTGGCAACCATTTCAGAGGAACAAG
TGATTATGATGATGTCCTAAGCTGCGAATACTATTCGCCAACTCTTGACCAGTGGACACCAATTGCTGCTATGCTAAGAG
GTCAGAGTGATGTTGGAGTTGCGGTCTTCGAAAACAAAATCTACGTTGTTGGTGGATATTCTTGGAATAACCGCTGCATG
GTAGAAATTGTCCAGAAATATGACCCAGAAAAAGATGAGTGGCATAAAGTTTTTGATCTTCCAGAGTCACTTGGTGGCAT
TCGGGCTTGCACTCTCACAGTTTTTCCACCTGAAGAAAACCCTGGGTCACCTTCTAGAGAATCACCTCTTTCAGCACCTT
CAGATCATTCTTAG

ORF - retro_rnor_154 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.05 %
Parental protein coverage: 95.92 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLKLCLGS-EMGLSSHLQSCKAGSTRIFTSNSHSSVVLQGFDQLRLDGLLCDVTLMPGDTDDAYPVHRVMM
.K..LG..EMG.S.HLQ.CKAG.TR.FTSN.HSSVVLQGFDQLR..GLLCDVTL.PGD.....PVHR.MM
RetrocopyMKVSLGNGEMGVSAHLQPCKAGTTRFFTSNTHSSVVLQGFDQLRIEGLLCDVTLVPGDGEEIFPVHRAMM
ParentalASASDYFKAMFTGGMKEQELMCIKLHGVSRVGLRKIIDFIYTAKLSLNMDTLQDTLEAASFLQILPVLDF
ASASDYFKAMFTGGMKE..LMCIKLHGV..VGL.KIIDFIYTAKLSLNMD.LQDTLEAASFLQILPVLDF
RetrocopyASASDYFKAMFTGGMKEKDLMCIKLHGVNKVGLKKIIDFIYTAKLSLNMDNLQDTLEAASFLQILPVLDF
ParentalCKVFLISGVTLDNCVEVGRIANTYHLTEVDKYVNSFVLKNFAALLSTGEFLKLPFERLAFVLSSNSLKRC
CKVFLISGV.LDNCVEVGRIANTY.L.EVDKYVN.F.LKNF.ALLSTGEFLKLPFERLAFVLSSNSLK.C
RetrocopyCKVFLISGVSLDNCVEVGRIANTYNLIEVDKYVNNFILKNFPALLSTGEFLKLPFERLAFVLSSNSLKHC
ParentalTELELFKATCRWLRLEEPRMDVAAKLMKNIRFPLMTPQELINYVQTVDFMRTDNTCVNLLLEASNYQMMP
.ELELFKA.CRWLRLE.PRMD.AAKLMKNIRFPLMTPQ.LINYVQTVDFMRTDNTCVNLLLEASNYQMMP
RetrocopySELELFKAACRWLRLEDPRMDYAAKLMKNIRFPLMTPQDLINYVQTVDFMRTDNTCVNLLLEASNYQMMP
ParentalFMQPVMQSDRTAIRSDTTHLVTLGGVLRQQLVVSKELRMYDEKTHEWKSLAPMDAPRYQHGIAVIGNFLY
.MQPVMQSDRTAIRSD.THLVTLGGVLRQQLVVSKELRMYDE...EWKSLAPMDAPRYQHGIAVIGNFLY
RetrocopyYMQPVMQSDRTAIRSDSTHLVTLGGVLRQQLVVSKELRMYDERAQEWKSLAPMDAPRYQHGIAVIGNFLY
ParentalVVGGQSNYDTKGKTAVDTVFRFDPRYNKWIQVASLNEKRTFFHLSALKGFLYAVGGRNAAGELPTVECYN
VVGGQSNYDTKGKTAVDTVFRFDPRYNKW.QVASLNEKRTFFHLSALKG.LYAVGGR.AAGEL.TVECYN
RetrocopyVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALKGHLYAVGGRSAAGELATVECYN
ParentalPRTNEWTYVAKMNEPHYGHAGTVYGGVMYISGGITHDTFQKELMCFDPDTDKWIQKAPMTTVRGLHCMCT
PR.NEW.YVAKM.EPHYGHAGTVYGG.MYISGGITHDTFQ.ELMCFDPDTDKW.QKAPMTTVRGLHCMCT
RetrocopyPRMNEWSYVAKMSEPHYGHAGTVYGGLMYISGGITHDTFQNELMCFDPDTDKWTQKAPMTTVRGLHCMCT
ParentalVGDRLYVIGGNHFRGTSDYDDVLSCEYYSPILDQWTPIASMLRGQSDVGVAVFENKIYVVGGYSWNNRCM
VGD.LYVIGGNHFRGTSDYDDVLSCEYYSP.LDQWTPIA.MLRGQSDVGVAVFENKIYVVGGYSWNNRCM
RetrocopyVGDKLYVIGGNHFRGTSDYDDVLSCEYYSPTLDQWTPIAAMLRGQSDVGVAVFENKIYVVGGYSWNNRCM
ParentalVEIVQKYDPEKNEWHKVFDLPESLGGIRACTLTVYPPEENTPSPSRESPLSGP
VEIVQKYDPEK.EWHKVFDLPESLGGIRACTLTV.PPEEN..SPSRESPLS.P
RetrocopyVEIVQKYDPEKDEWHKVFDLPESLGGIRACTLTVFPPEENPGSPSRESPLSAP

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 37 .31 RPM 60 .61 RPM
SRP017611_kidney 44 .66 RPM 10 .40 RPM
SRP017611_liver 23 .73 RPM 4 .17 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_154 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_154 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_154 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Mus musculus retro_mmus_121
Parental genes homology:
Parental genes homology involve 21 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000017821 retrocopy
retro_amel_749,
Bos taurus ENSBTAG000000005011 retrocopy
retro_btau_44,
Canis familiaris ENSCAFG000000182721 retrocopy
retro_cfam_422,
Callithrix jacchus ENSCJAG000000024471 retrocopy
retro_cjac_3406,
Cavia porcellus ENSCPOG000000112681 retrocopy
retro_cpor_590,
Equus caballus ENSECAG000000082371 retrocopy
retro_ecab_622,
Loxodonta africana ENSLAFG000000081221 retrocopy
retro_lafr_1018,
Myotis lucifugus ENSMLUG000000273931 retrocopy
retro_mluc_204,
Macaca mulatta ENSMMUG000000022931 retrocopy
retro_mmul_42,
Mustela putorius furoENSMPUG000000017301 retrocopy
retro_mputfur_169,
Mus musculus ENSMUSG000000367821 retrocopy
retro_mmus_121,
Nomascus leucogenys ENSNLEG000000147361 retrocopy
retro_nleu_1031,
Oryctolagus cuniculus ENSOCUG000000019931 retrocopy
retro_ocun_254,
Pongo abelii ENSPPYG000000206581 retrocopy
retro_pabe_60,
Pteropus vampyrus ENSPVAG000000159891 retrocopy
retro_pvam_1485,
Rattus norvegicus ENSRNOG00000014029 1 retrocopy
retro_rnor_154 ,
Sus scrofa ENSSSCG000000126371 retrocopy
retro_sscr_51,
Ictidomys tridecemlineatus ENSSTOG000000120351 retrocopy
retro_itri_124,
Tarsius syrichta ENSTSYG000000025211 retrocopy
retro_tsyr_19,
Tursiops truncatus ENSTTRG000000140981 retrocopy
retro_ttru_26,
Vicugna pacos ENSVPAG000000030911 retrocopy
retro_vpac_8,




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