RetrogeneDB ID:

retro_cjac_3406

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01178277.1:12916..14818(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000022401
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KLHL9
Ensembl ID:ENSCJAG00000002447
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3406
AAAACATTCCGGTTATAACTTCTTTCTCCGGCCTGCATCTCTGTACAGGAGGAAAGCTTTCACATGAAAGTGTCCCTTGG
TAACGGCGAAATGGGCGTCTCTGCCCATTTGCAGCCTTGTAAGGCAGGAACCACACGCTTTTTTACCAGCAATACTCACA
GTTCGGTGGTACTGCAAGGCTTTGATCAGCTTAGAATAGAAGGATTGCTTTGTGATGTGACCCTCGTACCAGGTGATGGA
GATGAAATCTTCCCTGTTCACAGAGCTATGATGGCGTCTGCTAGTGATTATTTCAAGGCTATGTTCACAGGTGGAATGAA
AGAACAGGATTTGATGTGCATTAAACTTCATGGGGTGAACAAGGTTGGTCTGAAGAAAATCATTGATTTTATTTATACTG
CAAAACTTTCTCTTAATATGGACAGTCTTCAGGACACACTTGAAGCTGCCAGCTTTTTACAAATACTACCTGTTTTGGAC
TTCTGTAAAGTATTTCTTATATCAGGAGTCTCTTTAGATAACTGTGTTGAGGTTGGACGAATTGCTAACACCTACAATCT
TATAGAAGTGGATAAATATGTTAATAATTTCATCCTGAAGAACTTTCCTGCTTTACTGAGTACTGGAGAGTTTCTAAAAC
TCCCTTTTGAACGGCTTGCCTTTGTGCTTTCCAGTAACAGTCTTAAGCACTGTACCGAACTTGAACTCTTTAAGGCTGCC
TGTCGCTGGCTAAGGTTGGAAGACCCTCGGATGGATTATGCTGCAAAATTAATGAAGAATATTCGATTTCCACTGATGAC
ACCACAGGACCTCATCAATTACGTGCAGACGGTAGATTTCATGAGAACAGACAATACCTGTGTGAATCTGCTTTTGGAAG
CTAGCAATTACCAAATGATGCCATATATGCAGCCAGTGATGCAGTCAGATAGAACTGCCATTCGATCGGACTCCACTCAC
TTGGTTACATTAGGAGGAGTTTTGAGGCAGCAGCTAGTTGTCAGTAAAGAATTACGGATGTATGATGAAAGGGCACAAGA
ATGGAGATCTTTAGCCCCGATGGATGCTCCCCGTTACCAGCATGGCATTGCTGTCATTGGAAACTTTCTTTATGTAGTTG
GTGGTCAAAGTAATTACGATACAAAAGGAAAAACTGCTGTTGATACAGTTTTCAGGTTTGATCCTCGGTATAATAAATGG
ATGCAGGTTGCATCATTAAATGAAAAGCGCACATTCTTTCACTTGAGTGCCCTCAAAGGACATTTGTATGCAGTTGGTGG
GCGCAGTGCAGCTGGTGAACTAGCCACAGTAGAATGTTACAACCCAAGAATGAATGAGTGGAGCTATGTTGCAAAAATGA
GTGAACCCCACTATGGACATGCTGGAACAGTATATGGAGGCTTAATGTATATTTCAGGAGGAATTACCCATGACACTTTC
CAAAATGAGCTCATGTGTTTTGACCCAGATACAGACAAATGGATGCAAAAGGCTCCAATGACTACAGTCAGAGGTCTGCA
TTGCATGTGTACAGTTGGAGACAAGCTCTATGTCATTGGTGGCAATCACTTCAGAGGAACAAGTGATTATGATGATGTTC
TAAGCTGTGAATACTATTCACCAACCCTTGACCAGTGGACCCCAATTGCCGCCATGTTAAGAGGTCAAAGTGATGTTGGA
GTTGCCGTCTTTGAAAATAAAATCTACGTTGTTGGTGGATATTCTTGGAATAATCGTTGTATGGTAGAAATTGTCCAGAA
ATATGACCCAGAAAAAGATGAGTGGCATAAAGTTTTTGATCTCCCAGAGTCACTTGGTGGCATTCGAGCTTGTACACTCA
CAGTTTTTCCACCCGAAGAAAACCCTGGGTCACCTTCTAGAGAATCACCTCTTTCAGCACCT

ORF - retro_cjac_3406 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.34 %
Parental protein coverage: 96.95 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKTSRSTPLSPAYISLVEEEDQHMKLSLGGSEMGLSSHLQSSKAGPTRIFTSNTHSSVVLQGFDQLRLEGL
KT.R...LSPA.IS.V.EE..HMK.SLG..EMG.S.HLQ..KAG.TR.FTSNTHSSVVLQGFDQLR.EGL
RetrocopyKTFRL*LLSPACIS-VQEESFHMKVSLGNGEMGVSAHLQPCKAGTTRFFTSNTHSSVVLQGFDQLRIEGL
ParentalLCDVTLMPGDTDDAFPVHRVMMASASDYFKAMFTGGMKEQDLMCIKLHGVSKVGLRKIIDFIYTAKLSLN
LCDVTL.PGD.D..FPVHR.MMASASDYFKAMFTGGMKEQDLMCIKLHGV.KVGL.KIIDFIYTAKLSLN
RetrocopyLCDVTLVPGDGDEIFPVHRAMMASASDYFKAMFTGGMKEQDLMCIKLHGVNKVGLKKIIDFIYTAKLSLN
ParentalMDNLQDTLEAASFLQILPVLDFCKVFLISGVTLDNCVEVGRIANTYNLTEVDKYINSFVLKNFPALLSTG
MD.LQDTLEAASFLQILPVLDFCKVFLISGV.LDNCVEVGRIANTYNL.EVDKY.N.F.LKNFPALLSTG
RetrocopyMDSLQDTLEAASFLQILPVLDFCKVFLISGVSLDNCVEVGRIANTYNLIEVDKYVNNFILKNFPALLSTG
ParentalEFLKLPFERLAFVLSSNSLKHCTELELFKATCRWLRLEEPRMDFAAKLMKNIRFPLMTPQELINYVQTVD
EFLKLPFERLAFVLSSNSLKHCTELELFKA.CRWLRLE.PRMD.AAKLMKNIRFPLMTPQ.LINYVQTVD
RetrocopyEFLKLPFERLAFVLSSNSLKHCTELELFKAACRWLRLEDPRMDYAAKLMKNIRFPLMTPQDLINYVQTVD
ParentalFMRTDNTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSDTTHLVTLGGVLRQQLVVSKELRMYDEKAHEWK
FMRTDNTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSD.THLVTLGGVLRQQLVVSKELRMYDE.A.EW.
RetrocopyFMRTDNTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSDSTHLVTLGGVLRQQLVVSKELRMYDERAQEWR
ParentalSLAPMDAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALK
SLAPMDAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALK
RetrocopySLAPMDAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALK
ParentalGYLYAVGGRNAAGELPTVECYNPRTNEWTYVAKMSEPHYGHAGTVYGGVMYISGGITHDTFQKELMCFDP
G.LYAVGGR.AAGEL.TVECYNPR.NEW.YVAKMSEPHYGHAGTVYGG.MYISGGITHDTFQ.ELMCFDP
RetrocopyGHLYAVGGRSAAGELATVECYNPRMNEWSYVAKMSEPHYGHAGTVYGGLMYISGGITHDTFQNELMCFDP
ParentalDTDKWIQKAPMTTVRGLHCMCTVGERLYVIGGNHFRGTSDYDDVLSCEYYSPILDQWTPIAAMLRGQSDV
DTDKW.QKAPMTTVRGLHCMCTVG..LYVIGGNHFRGTSDYDDVLSCEYYSP.LDQWTPIAAMLRGQSDV
RetrocopyDTDKWMQKAPMTTVRGLHCMCTVGDKLYVIGGNHFRGTSDYDDVLSCEYYSPTLDQWTPIAAMLRGQSDV
ParentalGVAVFENKIYVVGGYSWNNRCMVEIVQKYDPDKDEWHKVFDLPESLGGIRACTLTVFPPEETTPSPSRES
GVAVFENKIYVVGGYSWNNRCMVEIVQKYDP.KDEWHKVFDLPESLGGIRACTLTVFPPEE...SPSRES
RetrocopyGVAVFENKIYVVGGYSWNNRCMVEIVQKYDPEKDEWHKVFDLPESLGGIRACTLTVFPPEENPGSPSRES
ParentalPLSAP
PLSAP
RetrocopyPLSAP

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
SRP051959_colon 19 .26 RPM 2 .33 RPM
SRP051959_heart 16 .40 RPM 7 .75 RPM
SRP051959_kidney 18 .59 RPM 13 .09 RPM
SRP051959_liver 13 .21 RPM 3 .47 RPM
SRP051959_lung 26 .87 RPM 12 .62 RPM
SRP051959_lymph_node 28 .79 RPM 0 .73 RPM
SRP051959_skeletal_muscle 8 .56 RPM 2 .14 RPM
SRP051959_spleen 29 .01 RPM 4 .60 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_3406 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3406 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3406 has 0 orthologous retrocopies within eutheria group .

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 ENSCJAG00000002447 1 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 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,


Copyright © RetrogeneDB 2014-2017