RetrogeneDB ID:

retro_cfam_422

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:11:40792534..40794441(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCAFG00000023674
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KLHL13
Ensembl ID:ENSCAFG00000018272
Aliases:None
Description:kelch-like family member 13 [Source:HGNC Symbol;Acc:22931]


Retrocopy-Parental alignment summary:






>retro_cfam_422
TTGAGAGCTTTCAGGCCACAGCCTCGTTCCCCGGGGGGCCCGGGTCTCCGCGGGAGGAAGGCTTTCCCATGAAAGTGTCC
CTCGGCACCGGCGAAATGGGCGTCTCCGCCCACCTACAGCCCTGCAAGGCAGGAACCACGCGTTTTTTTACCAGCAACAC
TCACAGTTCGGTGGTGCTGCAAGGCTTCGACCAGCTCAGAGTAGAAGGCTTGCTTTGTGATGTGACCCTGGTCCCGGGCG
ACGGAGATGAAATCTTCCCCGTTCACAGAGCTATGATGGCGTCCGCTAGTGATTACTTCAAGGCAATGTTCACAGGCGGA
ATGAAAGAACAGGATCTGATGTGCATTAAGCTGCATGGGGTGAACAAGGTTGGGCTGAAGAAAATAATTGATTTCATTTA
TACTGCAAAACTTTCTCTCAATATGGACAATCTTCAGGACACCCTTGAAGCTGCCAGCTTCTTACAGATTTTGCCCGTCT
TGGACTTCTGTAAGGTGTTCCTTATTTCGGGAGTCTCTTTAGACAACTGTGTTGAAGTTGGGCGGATTGCTAACACCTAC
AATCTGATCGAAGTGGATAAGTACGTCAATAATTTCATCCTGAAGAATTTTCCTGCATTGCTGAGTACCGGGGAGTTTCT
AAAACTCCCCTTTGAACGGCTTGCCTTTGTGCTTTCTAGTAACAGCCTTAAGCACTGTACTGAACTTGAGCTCTTCAAGG
CCGCCTGTCGCTGGCTAAGATTGGAAGACCCTCGGATGGATTATGCTGCAAAATTAATGAAGAACATTCGATTTCCATTG
ATGACACCCCAGGATCTCATCAATTACGTGCAGACAGTAGATTTCATGAGAACAGACAATACTTGTGTGAATTTGCTTTT
GGAAGCTAGCAATTACCAAATGATGCCATATATGCAGCCAGTGATGCAGTCAGATAGAACTGCCATTCGATCTGACTCGA
CACACTTGGTCACATTAGGAGGAGTTTTGAGGCAGCAGCTGGTTGTCAGCAAAGAATTACGGATGTATGACGAAAGGGCA
CAAGAGTGGAGATCTCTTGCCCCCATGGATGCTCCTCGTTACCAGCATGGTATTGCTGTCATTGGAAACTTTCTTTATGT
AGTTGGTGGTCAAAGTAATTATGATACGAAAGGGAAAACTGCTGTTGATACAGTTTTCAGGTTTGATCCTCGGTACAACA
AATGGATGCAGGTTGCATCGTTAAATGAAAAGCGCACGTTTTTCCACTTGAGTGCCCTTAAAGGACATTTATATGCTGTT
GGTGGGCGAAGTGCGGCTGGTGAACTGGCCACAGTAGAATGTTACAACCCAAGGATGAATGAGTGGAGCTATGTTGCAAA
AATGAGCGAGCCCCACTATGGCCATGCTGGAACAGTGTACGGAGGCTTGATGTATATTTCAGGAGGAATTACTCATGACA
CTTTCCAAAACGAGCTCATGTGTTTTGACCCAGATACAGACAAATGGACACAGAAGGCTCCAATGACTACAGTCCGAGGT
CTGCACTGCATGTGTACAGTTGGAGACAAGCTCTATGTCATTGGTGGCAATCACTTCAGAGGAACAAGTGATTATGATGA
TGTTCTAAGCTGTGAATACTATTCACCAACCCTTGACCAGTGGACACCAATTGCTGCTATGTTAAGAGGTCAGAGTGATG
TTGGAGTTGCTGTCTTTGAAAATAAAATCTATGTTGTGGGTGGATATTCCTGGAATAATCGTTGTATGGTAGAAATTGTC
CAGAAATATGACCCAGAAAAGGATGAATGGCATAAAGTTTTTGACCTTCCAGAGTCACTTGGTGGGATTCGAGCTTGTAC
TCTCACAGTTTTTCCACCCGAGGAAAACCCTGGGTCACCTTCTAGAGAATCCCCTCTTTCAGCACCT

ORF - retro_cfam_422 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.74 %
Parental protein coverage: 97.1 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLKTSRSTPLSPAYISL-VEEEDQHMKLSLGSSEMGLSSHLQSSKAGTTRIFTSNTHSSVVLQGFDQLRLE
L...R..P.SP....L...EE...MK.SLG..EMG.S.HLQ..KAGTTR.FTSNTHSSVVLQGFDQLR.E
RetrocopyLRAFRPQPRSPGGPGL<PREEGFPMKVSLGTGEMGVSAHLQPCKAGTTRFFTSNTHSSVVLQGFDQLRVE
ParentalGLLCDVTLMPGDTDDAFPVHRVMMASASDYFKAMFTGGMKEQDLMCIKLHGVSKVGLRKIIDFIYTAKLS
GLLCDVTL.PGD.D..FPVHR.MMASASDYFKAMFTGGMKEQDLMCIKLHGV.KVGL.KIIDFIYTAKLS
RetrocopyGLLCDVTLVPGDGDEIFPVHRAMMASASDYFKAMFTGGMKEQDLMCIKLHGVNKVGLKKIIDFIYTAKLS
ParentalLNMDNLQDTLEAASFLQILPVLDFCKVFLISGVTLDNCVEVGRIANTYNLTEVDKYVNSFVLKNFPALLS
LNMDNLQDTLEAASFLQILPVLDFCKVFLISGV.LDNCVEVGRIANTYNL.EVDKYVN.F.LKNFPALLS
RetrocopyLNMDNLQDTLEAASFLQILPVLDFCKVFLISGVSLDNCVEVGRIANTYNLIEVDKYVNNFILKNFPALLS
ParentalTGEFLKLPFERLAFVLSSNSLKHCTELELFKATCRWLRLEEPRMDFAAKLMKNIRFPLMTPQELINYVQT
TGEFLKLPFERLAFVLSSNSLKHCTELELFKA.CRWLRLE.PRMD.AAKLMKNIRFPLMTPQ.LINYVQT
RetrocopyTGEFLKLPFERLAFVLSSNSLKHCTELELFKAACRWLRLEDPRMDYAAKLMKNIRFPLMTPQDLINYVQT
ParentalVDFMRTDNTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSDTTHLVTLGGVLRQQLVVSKELRMYDEKAHE
VDFMRTDNTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSD.THLVTLGGVLRQQLVVSKELRMYDE.A.E
RetrocopyVDFMRTDNTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSDSTHLVTLGGVLRQQLVVSKELRMYDERAQE
ParentalWKSLAPMDAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSA
W.SLAPMDAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSA
RetrocopyWRSLAPMDAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSA
ParentalLKGYLYAVGGRNAAGELPTVECYNPRTNEWTYVAKMSEPHYGHAGTVYGGVMYISGGITHDTFQKELMCF
LKG.LYAVGGR.AAGEL.TVECYNPR.NEW.YVAKMSEPHYGHAGTVYGG.MYISGGITHDTFQ.ELMCF
RetrocopyLKGHLYAVGGRSAAGELATVECYNPRMNEWSYVAKMSEPHYGHAGTVYGGLMYISGGITHDTFQNELMCF
ParentalDPDTDKWIQKAPMTTVRGLHCMCTVGERLYVIGGNHFRGTSDYDDVLSCEYYSPILDQWTPIAAMLRGQS
DPDTDKW.QKAPMTTVRGLHCMCTVG..LYVIGGNHFRGTSDYDDVLSCEYYSP.LDQWTPIAAMLRGQS
RetrocopyDPDTDKWTQKAPMTTVRGLHCMCTVGDKLYVIGGNHFRGTSDYDDVLSCEYYSPTLDQWTPIAAMLRGQS
ParentalDVGVAVFENKIYVVGGYSWNNRCMVEIVQKYDPDKDEWHKVFDLPESLGGIRACTLTVFPPEETTPSPSR
DVGVAVFENKIYVVGGYSWNNRCMVEIVQKYDP.KDEWHKVFDLPESLGGIRACTLTVFPPEE...SPSR
RetrocopyDVGVAVFENKIYVVGGYSWNNRCMVEIVQKYDPEKDEWHKVFDLPESLGGIRACTLTVFPPEENPGSPSR
ParentalESPLSAP
ESPLSAP
RetrocopyESPLSAP

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
SRP012049_cerebellum 40 .57 RPM 24 .36 RPM
SRP017611_brain 25 .48 RPM 22 .39 RPM
SRP017611_kidney 22 .91 RPM 7 .79 RPM
SRP017611_liver 11 .17 RPM 0 .15 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_422 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_422 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_422 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 20 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000017821 retrocopy
retro_amel_749,
Bos taurus ENSBTAG000000005011 retrocopy
retro_btau_44,
Canis familiaris ENSCAFG00000018272 1 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,
Rattus norvegicus ENSRNOG000000140291 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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