RetrogeneDB ID:

retro_cpor_590

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_2:447560..449417(-)
Located in intron of:ENSCPOG00000009134
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KLHL13
Ensembl ID:ENSCPOG00000011268
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_590
CAAAAGGAAAGCTTTCACATGAAAGTGTCTCTTGGTAACGGCGATATGGGCGTCTCTGCCCACTTGCAGCCTTGTAAGGC
AGGAACTACAAGATTTTTTACCAGCAATACTCATAGTTCGGTGGTATTGCAAGGCTTTGATCAGCTAAGAATAGAAGGAT
TGCTCTGTGATGTGACCCTGGTACCCGGTGATGGAGATGAAATCTTCCCTGTTCACCGAGCTATGATGGCGTCTGCCAGT
GATTATTTCAAGGCTATGTTCACAGGTGGAATGAAAGAACAAGATTTAATGTGCATTAAGCTTCATGGGGTGAACAAAGT
TGGTCTGAAGAAAATAATTGATTTTATATATACTGCAAAACTGTCTCTTAATATGGACAATCTTCAGGACACACTAGAAG
CTGCCAGCTTTTTACAAATTTTGCCTGTTTTGGACTTCTGCAAAGTATTTCTTATATCAGGAGTCTCTTTGGATAACTGT
GTTGAGGTTGGACGAATTGCTAACACGTATAATCTCATAGAAGTAGATAAATATGTTAATAATTTCATCCTAAAGAACTT
TCCTGCTTTATTGAGTACTGGGGAGTTTCTAAAACTTCCTTTTGAACGGCTTGCCTTTGTGCTTTCCAGTAATAGTCTTA
AGCATTGTACTGAACTTGAACTCTTCAAGGCTGCCTGCCGTTGGCTGAGACTGGAAGACCCTCGGATGGATTATGCAGCA
AAATTAATGAAGAATATTCGATTTCCACTGATGACACCACAAGACCTCATCAATTATGTGCAGACAGTTGATTTCATGAG
AACAGACAATACCTGTGTGAATTTGCTTTTGGAAGCTAGCAATTACCAAATGATGCCTTATATGCAGCCAGTGATGCAGT
CAGACAGAACTGCTATTCGATCTGATTCTACTCACTTGGTTACATTAGGAGGAGTTTTGAGGCAGCAGCTGGTTGTTAGT
AAAGAATTACGGATGTATGATGAAAGAGCTCAAGAGTGGAGAGCCTTAGCCCCTATGGATGCTCCTCGTTACCAGCATGG
CATTGCTGTCATTGGAAACTTCCTTTATGTAGTTGGTGGTCAGAGTAATTATGATACAAAAGGAAAAACTGCTGTTGATA
CAGTTTTCAGATTTGATCCTCGGTATAATAAATGGATGCAGGTAGCATCGTTAAATGAAAAGCGCACATTCTTCCACTTG
AGTGCCCTCAAAGGACATTTATATGCAGTTGGTGGGCGCAGTGCAGCTGGTGAACTGGCCACAGTAGAATGTTACAATCC
AAGAATGAATGAATGGAGCTATGTTGCAAAAATGAGTGAACCCCACTATGGGCATGCTGGAACAGTGTATGGAGGCTTAA
TGTATATTTCTGGAGGAATTACCCACGACACTTTTCAAAATGAGCTTATGTGTTTTGATCCAGATACAGACAAATGGACA
CAGAAGGCTCCAATGACTACAGTCAGAGGTCTGCATTGCATGTGTACAGTTGGAGATAAGCTCTATGTCATTGGTGGCAA
CCATTTCAGAGGAACAAGTGATTATGATGATGTTCTAAGCTGTGAATACTATTCACCAACCCTTGACCAATGGACACCAA
TTGCTGCTATGTTAAGAGGTCAAAGTGATGTTGGAGTTGCTGTCTTTGAAAACAAAATCTATGTTGTTGGTGGATATTCG
TGGAATAACCGTTGTATGGTAGAAATTGTCCAGAAGTATGACCCAGAAAAAGATGAGTGGCATAAGGTTTTTGATCTTCC
AGAGTCACTTGGTGGCATTCGAGCTTGTACCCTCACTGTTTTTCCACCTGAAGAAAACCCTGGCTCACCTTCTAGAGAAT
CACCTCTTTCAGCACCT

ORF - retro_cpor_590 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.76 %
Parental protein coverage: 94.5 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEEDDQHMRLSLGSSEMGLSSHLQSSKAGTTRIFTSNTHSSVVLQGFDQLRLEGLLCDVTLMPGDTDDAFP
.....HM..SLG...MG.S.HLQ..KAGTTR.FTSNTHSSVVLQGFDQLR.EGLLCDVTL.PGD.D..FP
RetrocopyQKESFHMKVSLGNGDMGVSAHLQPCKAGTTRFFTSNTHSSVVLQGFDQLRIEGLLCDVTLVPGDGDEIFP
ParentalVHRVMMASASDYFKAMFTGGMKEQDLMCIKLHGVSKVGLRKIIDFIYTAKLSLNMDNLQDTLEAASFLQI
VHR.MMASASDYFKAMFTGGMKEQDLMCIKLHGV.KVGL.KIIDFIYTAKLSLNMDNLQDTLEAASFLQI
RetrocopyVHRAMMASASDYFKAMFTGGMKEQDLMCIKLHGVNKVGLKKIIDFIYTAKLSLNMDNLQDTLEAASFLQI
ParentalLPVLDFCKVFLISGVTLDNCVEVGRIANTYNLTEVDKYVNSYVLKNFPALLSTGEFLKLPFERLAFVLSS
LPVLDFCKVFLISGV.LDNCVEVGRIANTYNL.EVDKYVN...LKNFPALLSTGEFLKLPFERLAFVLSS
RetrocopyLPVLDFCKVFLISGVSLDNCVEVGRIANTYNLIEVDKYVNNFILKNFPALLSTGEFLKLPFERLAFVLSS
ParentalNSLKHCTELELFKATCRWLRLEEPRMDFAAKLMKNIRFPLMTPQELINYVQTVDFMRTDNTCVNLLLEAS
NSLKHCTELELFKA.CRWLRLE.PRMD.AAKLMKNIRFPLMTPQ.LINYVQTVDFMRTDNTCVNLLLEAS
RetrocopyNSLKHCTELELFKAACRWLRLEDPRMDYAAKLMKNIRFPLMTPQDLINYVQTVDFMRTDNTCVNLLLEAS
ParentalNYQMMPYMQPVMQSDRTAIRSDTTHLVTLGGVLRQQLVVSKELRMYDEKAHEWRSLAPMDAPRYQHGIAV
NYQMMPYMQPVMQSDRTAIRSD.THLVTLGGVLRQQLVVSKELRMYDE.A.EWR.LAPMDAPRYQHGIAV
RetrocopyNYQMMPYMQPVMQSDRTAIRSDSTHLVTLGGVLRQQLVVSKELRMYDERAQEWRALAPMDAPRYQHGIAV
ParentalIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALKGYLYAVGGRNAAGELP
IGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALKG.LYAVGGR.AAGEL.
RetrocopyIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALKGHLYAVGGRSAAGELA
ParentalTVECYNPRTNEWTYVAKMSEPHYGHAGTVYGGVMYISGGITHDTFQKELMCFDPDTDKWIQKAPMTTVRG
TVECYNPR.NEW.YVAKMSEPHYGHAGTVYGG.MYISGGITHDTFQ.ELMCFDPDTDKW.QKAPMTTVRG
RetrocopyTVECYNPRMNEWSYVAKMSEPHYGHAGTVYGGLMYISGGITHDTFQNELMCFDPDTDKWTQKAPMTTVRG
ParentalLHCMCTVGERLYVIGGNHFRGTSDYDDVLSCEYYSPILDQWTPIAAMLRGQSDVGVAVFENKIYVVGGYS
LHCMCTVG..LYVIGGNHFRGTSDYDDVLSCEYYSP.LDQWTPIAAMLRGQSDVGVAVFENKIYVVGGYS
RetrocopyLHCMCTVGDKLYVIGGNHFRGTSDYDDVLSCEYYSPTLDQWTPIAAMLRGQSDVGVAVFENKIYVVGGYS
ParentalWNNRCMVEIVQKYDPDKDEWHKVFDLPESLGGIRACTLTVFPPEETTPSPSRESPLSAP
WNNRCMVEIVQKYDP.KDEWHKVFDLPESLGGIRACTLTVFPPEE...SPSRESPLSAP
RetrocopyWNNRCMVEIVQKYDPEKDEWHKVFDLPESLGGIRACTLTVFPPEENPGSPSRESPLSAP

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 34 .16 RPM 19 .90 RPM
SRP017611_kidney 26 .70 RPM 21 .57 RPM
SRP017611_liver 17 .06 RPM 1 .18 RPM
SRP040447_lung 39 .65 RPM 11 .27 RPM
SRP040447_skeletal_muscle 11 .18 RPM 17 .40 RPM

ChIP-Seq - click to see more details

Cavia porcellus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cpor_590 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_590 was not experimentally validated.

Retrocopy orthology:
Cavia porcellus 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 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 ENSCPOG00000011268 1 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 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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