RetrogeneDB ID:

retro_cjac_4039

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:X:2220852..2222760(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000015833
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_4039
ATGAACCCCAGCGCACGCAGCTTCCTCATGGCCCCGCTCTACGTGGGGGACCTCCACCCAGACGTGACCGAAACGATGCT
CTATGACAAGTTCTGCCCGGTCGGGCCTATCCTCTCCATCCGGGTCTGCAGGGACTCGATCACTGGCCGCTCCTTGGGCT
ACGCGTATGTGAACTTCCAGCAGCCGCTGGACGCGGATCGTGCTTTGAATACCATGAATTTTGATGTTATAAAGGGCAAG
CCACTACGCATCATGTGGTCTCACCGTGATCCATCACTTCGCAAAAGTGGAGTGGGCAACATATTTATTAAAAATCTGGA
CAAATCCATTGATAGTAAAGCACTGTATGATACATTTTCTACTTTTGGTAACATCCTCTCATGTAAGTTGGTTTGTGATG
AAAACGGTTCCAAGGGCTATGGATTTGTACACTTTGAGACACAGGAAGCAGCTAAAACTGCTATTGAAAAAATGAATGGA
ATGCTCCTAAACGATCGCAAAGTATTTGTTGGACCATTTAAGTCTCGTAAAGAACGAGAAGCTGAATTTGAAGCTAGGGC
AAAAGAGTTCACCAATGTTTACATCAAGAATTTTGGAGAAGACATGGACAATGAGGGCCTTAAGGATCTCTTTGGCAAGT
TTGGGCCTGTCTTAAGTGTGAAAGTGATGACTGACGGAAGTGGAAAATCCAAAGGATTTGGATTTGTAAACTTTAAAAGG
CATGAAGATGCACAGAAAGCTGTGGATGAGATGAATGGAAATGAGCTCAATGGAAAACAAATTTACGTTGGTCGAGCTCA
GCCAAAGTGGGAACGGCAAATAAAACTTAAGCGCAAATTTGAACAGATGAAGCACGACAGGAACACCAGATATAAGGGTG
TTAATCTTTATGTGAAAAACCTTGATGATAGTATTGATGATGAACGCCTCCGGAAAGAGTTTTCTCCATTTGGCACAATC
AGGAGTGCAAAGGTTATGATGGACGGTGATCGCAGCAAAGGGTTTGGTTTCGTATGTTTCTCCTCCCCAGAAGAAGCCAT
TAAAGCACTTACAAACATGAAAGGTAGAATTCTGGCCACAAAGCCACTGTATGTAGCTTTAGCTCAGCACAAACAAGAGC
GCCAGGCTCGCCTCACTAACAAGTATATGCAGAGAATGGCAAGTGTACGAGCTGTGCCCAACCCTGTGATCAACCCCCAC
CAGCCAGCACCTCCTTCAGATTATTTCACGGCGGTTCTCCCACAGACTCAGAACCGGGCTGCATACTACCTTCCTAGCCA
AATTGTTCAACTAAGACCGAATCCTTGCTGGATTGCTCAGCGTGGCAGACCTCATCCATTCCAAAATATGCCCAGGACTA
TCCACCCAGCTGCTGCTAGACTACCATTTAGTACTATGACACCAGCTTTTCCACAGGTTCCACGGGTCATGTCAACACAG
CGTGTTGCTAACACAACAATGCAGAGGATGGGCCCATGTCCTGCAGCTGCAGCTGCTGCAGCTACTCCTGCTGTCTGCAC
CTTTCCACAGTATAAATATGCTGTGGGAATTCGCAGTCCTCAGCAACATCTTCATGCACAGCCACAAGTTAGAGTGCAAC
AGCCTGCTGTTCATGTACAAGGTCAAGAATCTTTCACCGCTTCCATGTTGGCATCTCCCCCTACTCAAGAGCAAAAGTAA
ATGTTGGGTGAACGGCTGTTTCCTCTTACTCAAGCCATGCACCCTACTCTTGCTGGTAAAATCCCTGGCATGTCGTTGGA
GATGGATAATTCAGAACTTCTTCATATGCTCGAGTCTCCAGAGTCACTCCGTTCTAAGGTTGACGAAGCTGTAGCTGTAC
TACGAGCCCACCAAGCCAAAGAGGCTGCCCAGAAAGCGGTTAACAGCGCCACCTGTGTTCCGATTGTT

ORF - retro_cjac_4039 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.06 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD
MNPSA.S..MA.LYVGDLHPDVTE.MLY.KF.P.GPILSIRVCRD.IT.RSLGYAYVNFQQP.DA.RAL.
RetrocopyMNPSARSFLMAPLYVGDLHPDVTETMLYDKFCPVGPILSIRVCRDSITGRSLGYAYVNFQQPLDADRALN
ParentalTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
TMNFDVIKGKP.RIMWS.RDPSLRKSGVGNIFIKNLDKSID.KALYDTFS.FGNILSCK.VCDENGSKGY
RetrocopyTMNFDVIKGKPLRIMWSHRDPSLRKSGVGNIFIKNLDKSIDSKALYDTFSTFGNILSCKLVCDENGSKGY
ParentalGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDL
GFVHFETQEAA..AIEKMNGMLLNDRKVFVG.FKSRKEREAE..ARAKEFTNVYIKNFGEDMD.E.LKDL
RetrocopyGFVHFETQEAAKTAIEKMNGMLLNDRKVFVGPFKSRKEREAEFEARAKEFTNVYIKNFGEDMDNEGLKDL
ParentalFGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKF
FGKFGP.LSVKVMTD.SGKSKGFGFV.F.RHEDAQKAVDEMNG.ELNGKQIYVGRAQ.K.ERQ..LKRKF
RetrocopyFGKFGPVLSVKVMTDGSGKSKGFGFVNFKRHEDAQKAVDEMNGNELNGKQIYVGRAQPKWERQIKLKRKF
ParentalEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV
EQMK.DR.TRY.GVNLYVKNLDD.IDDERLRKEFSPFGTI.SAKVMM.G.RSKGFGFVCFSSPEEA.KA.
RetrocopyEQMKHDRNTRYKGVNLYVKNLDDSIDDERLRKEFSPFGTIRSAKVMMDGDRSKGFGFVCFSSPEEAIKAL
ParentalTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRA
T.M.GRI.ATKPLYVALAQ.K.ERQA.LTN.YMQRMASVRAVPNPVINP.QPAPPS.YF.A..PQTQNRA
RetrocopyTNMKGRILATKPLYVALAQHKQERQARLTNKYMQRMASVRAVPNPVINPHQPAPPSDYFTAVLPQTQNRA
ParentalAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQRVANTSTQTM
AYY.PSQI.QLRP.P.W.AQ..RPHPFQNMP..I.PAA.R.PFSTM.PA..QVPRVMSTQRVANT..Q.M
RetrocopyAYYLPSQIVQLRPNPCWIAQRGRPHPFQNMPRTIHPAAARLPFSTMTPAFPQVPRVMSTQRVANTTMQRM
ParentalGPRPAAAAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQ
GP.PAAAAAAATPAV.T.PQYKYA.G.R.PQQHL.AQPQV..QQPAVHVQGQE..TASMLAS.P.QEQK.
RetrocopyGPCPAAAAAAATPAVCTFPQYKYAVGIRSPQQHLHAQPQVRVQQPAVHVQGQESFTASMLASPPTQEQK*
ParentalMLGERLFPLIQAMHPSLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAAQKAVNSA
MLGERLFPL.QAMHP.LAGKI.GM.LE.DNSELLHMLESPESLRSKVDEAVAVL.AHQAKEAAQKAVNSA
RetrocopyMLGERLFPLTQAMHPTLAGKIPGMSLEMDNSELLHMLESPESLRSKVDEAVAVLRAHQAKEAAQKAVNSA
ParentalTGVPTV
T.VP.V
RetrocopyTCVPIV

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 0 .00 RPM 64 .39 RPM
SRP051959_heart 0 .00 RPM 55 .83 RPM
SRP051959_kidney 0 .00 RPM 49 .21 RPM
SRP051959_liver 0 .00 RPM 70 .90 RPM
SRP051959_lung 0 .05 RPM 87 .34 RPM
SRP051959_lymph_node 0 .00 RPM 84 .11 RPM
SRP051959_skeletal_muscle 0 .00 RPM 31 .93 RPM
SRP051959_spleen 0 .02 RPM 123 .49 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_4039 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_4039 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_4039 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 26 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000003481 retrocopy
retro_amel_1650,
Choloepus hoffmanni ENSCHOG000000081781 retrocopy
retro_chof_2531,
Callithrix jacchus ENSCJAG000000025123 retrocopies
retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Callithrix jacchus ENSCJAG000000108031 retrocopy
retro_cjac_1022,
Callithrix jacchus ENSCJAG000000148611 retrocopy
retro_cjac_1040,
Callithrix jacchus ENSCJAG00000015833 5 retrocopies
retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039 , retro_cjac_41,
Cavia porcellus ENSCPOG000000129171 retrocopy
retro_cpor_1324,
Dasypus novemcinctus ENSDNOG000000087182 retrocopies
retro_dnov_1530, retro_dnov_2259,
Felis catus ENSFCAG000000018741 retrocopy
retro_fcat_1927,
Homo sapiens ENSG000000707561 retrocopy
retro_hsap_88,
Gorilla gorilla ENSGGOG000000067851 retrocopy
retro_ggor_1986,
Myotis lucifugus ENSMLUG000000122451 retrocopy
retro_mluc_579,
Macaca mulatta ENSMMUG000000177862 retrocopies
retro_mmul_1462, retro_mmul_895,
Monodelphis domestica ENSMODG000000062224 retrocopies
retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus ENSMUSG000000222832 retrocopies
retro_mmus_102, retro_mmus_2164,
Nomascus leucogenys ENSNLEG000000031423 retrocopies
retro_nleu_221, retro_nleu_2412, retro_nleu_611,
Oryctolagus cuniculus ENSOCUG000000043541 retrocopy
retro_ocun_13,
Pongo abelii ENSPPYG000000187903 retrocopies
retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus ENSPVAG000000166402 retrocopies
retro_pvam_10, retro_pvam_855,
Rattus norvegicus ENSRNOG000000086393 retrocopies
retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii ENSSHAG000000112671 retrocopy
retro_shar_24,
Sus scrofa ENSSSCG000000060632 retrocopies
retro_sscr_1153, retro_sscr_1205,
Ictidomys tridecemlineatus ENSSTOG000000163952 retrocopies
retro_itri_139, retro_itri_48,
Tarsius syrichta ENSTSYG000000042292 retrocopies
retro_tsyr_1743, retro_tsyr_273,
Tursiops truncatus ENSTTRG000000046892 retrocopies
retro_ttru_1050, retro_ttru_1812,
Vicugna pacos ENSVPAG000000038654 retrocopies
retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,


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