RetrogeneDB ID:

retro_cjac_1046

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:12:74110766..74112363(-)
Located in intron of:ENSCJAG00000005222
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:WDR1
Ensembl ID:ENSCJAG00000011293
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1046
TTCTACATCGCCTCCAGAGCTGTGACTGGGAAGCTGAGAATCTGGGAAACCACGCAGAAGGAGCACCTGTTGAGAACGAG
TACCAGCCTTTCGCCAGGAAGATCAAAGACATTGCCTGGACTTAAGACAGTAAGAGGATCGCCGTGGTCGGGGAAGGAAG
GGAGAAGTTCGGAGCAGTCTTCCTGTGGGATAGTGGCTCTTCTGTGGGCGAGATCACGGGCCACAACAAAGTCATCAACA
GTGTGGACATCAAGCAAAGCCGGCCATACTGGTTGGCCACAGGAAGCGACGATAACTGCGCTGCATTCTTTGAGGGACCC
CCATTCGAGTTCAATATCACAATTGGTGACCACAGCCGCTTTGTCAACTGTGTGCGATTCTCTCCTGATGGGAACAGATT
TGCCACAGCCATTGCTGACGGCCAGATATACATCTATGACAGGAAAACTGGGGAGAAGGTGTGCGCACTGGGCGGAAGCA
AGGCCCACAACGGCAGGATTTACACCATTAGTTGGAGTCCTGACAGCACCCATCTGCTTTCTGTTTCTGGGTACAAAACT
TACAAGATCTGGACATGGACTCCATGGTCAGTGTGTTTCCCATGGGCTCCAGGGTTCTGGACCAGCAGCTGGGCTGCCTG
TGGCAGAAGGACCACCTGCTCAGTGTCTCCCTGTCTGGGTACATCAACTATCTGGACAGAAACAACCCCAGCAAGCCCGT
GTCCGACATCAAGGGTCACAGTAAATCAATCCAGTGTCTGACCGTGCATAAAAACGGCAGCAAGTCCTACATCTACTCCA
GGAGCCACGATGGACACATTAATTACTGGGATTCAGAGACAGGGGAGAACGACTCCTACACTGGGAAGTGCCACATGAAC
CAGGTGTCCAGGATGACCGTGGACGAGTCGGGGCAGCTCATCAGCTGCAGCGTTGACGACACCGTGCGTTACACCAACCT
TACACTGCGGGACTACAGTGGACAAGGAGTCATGAAACTGGACGTTCAGCCAAAGTGTGTCATTGTGGGCCCTGGGGGAT
ACGCTGTGGTCATGTGCATCGGGCAGATCGTCCTGCTGAGGGATCAGAGGAAGTGTTTCAGCATCAACAGCCCCGGCTAC
GAGCCTGAAGTTGTGGCAGTGCACCCAGGCGGGGACACGGTGGTGATTAGAGGTGTGGATGGCAGCGTCCGCCTGTACTC
CATCCTGGGTACCATGCTGAAGGATGAGGGCAAGCTCCTAGAGGCCAAGGGCCCTGTGACTGACGTGACCTACTCCCACG
ATGGCGCCTTCCTTGCCGTGTGCGACGCCAGCAGGTGATCACAGTGTTTAGCGTTGCTGACGGGCTACTCGAGCAGTGTT
TTTTATGGACACCGTGCAAAAATCGTCTGCCTGGCCTGATTCCCAGACAATGAACACTTTGCCTCTGGTGTCATGGACAT
GATGGTGTACATCTGGACCCTAAGTGACCCAGAAACCAGAGTTGAGATCCAAGATGCACACCGGCTGTACCATGTCAGCA
GCCTGGCCTGGCTGGACGAGCACACGCTGGTCACCACCTCCCACGATGCCTCTGTCAAGGATTGAACAATCACCTAC

ORF - retro_cjac_1046 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.85 %
Parental protein coverage: 85.9 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalFYIASGDVSGKLRIWDTTQKEHLLKY-EYQPFAGKIKDIAWTEDSKRIAVVGEGREKFGAVFLWDSGSSV
FYIAS..V.GKLRIW.TTQKEHLL...EYQPFA.KIKDIAWT.DSKRIAVVGEGREKFGAVFLWDSGSSV
RetrocopyFYIASRAVTGKLRIWETTQKEHLLRT<EYQPFARKIKDIAWT*DSKRIAVVGEGREKFGAVFLWDSGSSV
ParentalGEITGHNKVINSVDIKQSRPYRLATGSDDNCAAFFEGPPFKFKFTIGDHSRFVNCVRFSPDGNRFATASA
GEITGHNKVINSVDIKQSRPY.LATGSDDNCAAFFEGPPF.F..TIGDHSRFVNCVRFSPDGNRFATA.A
RetrocopyGEITGHNKVINSVDIKQSRPYWLATGSDDNCAAFFEGPPFEFNITIGDHSRFVNCVRFSPDGNRFATAIA
ParentalDGQIYIYDGKTGEKVCALGGSKAHDGGIYAXSWSPDSTHLLSASGDKTSKIWDVNVNSVVSVFP-MGTTV
DGQIYIYD.KTGEKVCALGGSKAH.G.IY..SWSPDSTHLLS.SG.KT.KIW.....SV...FP.MG..V
RetrocopyDGQIYIYDRKTGEKVCALGGSKAHNGRIYTISWSPDSTHLLSVSGYKTYKIWTWTPWSV--CFP<MGSRV
ParentalLDQQLGCLWQKDHLLSVSLSGYINYLDRNNPSKPLRVIKGHSKSIQCLTVHKNGGKSYIYSGSHDGHINY
LDQQLGCLWQKDHLLSVSLSGYINYLDRNNPSKP...IKGHSKSIQCLTVHKNG.KSYIYS.SHDGHINY
RetrocopyLDQQLGCLWQKDHLLSVSLSGYINYLDRNNPSKPVSDIKGHSKSIQCLTVHKNGSKSYIYSRSHDGHINY
ParentalWDSETGENDSFAGKGHTNQVSRMTVDESGQLISCSMDDTVRYTNLTLRDYSGQAVVKLDVQPKCVAVGPG
WDSETGENDS..GK.H.NQVSRMTVDESGQLISCS.DDTVRYTNLTLRDYSGQ.V.KLDVQPKCV.VGPG
RetrocopyWDSETGENDSYTGKCHMNQVSRMTVDESGQLISCSVDDTVRYTNLTLRDYSGQGVMKLDVQPKCVIVGPG
ParentalGYAVVVCIGQIVLLKDQRKCFSIDSPGYEPEVVAVHPGGDTVAVGGADGSVRLYSILGTTLKDEGKLLEA
GYAVV.CIGQIVLL.DQRKCFSI.SPGYEPEVVAVHPGGDTV...G.DGSVRLYSILGT.LKDEGKLLEA
RetrocopyGYAVVMCIGQIVLLRDQRKCFSINSPGYEPEVVAVHPGGDTVVIRGVDGSVRLYSILGTMLKDEGKLLEA
ParentalKGPVTDVAYSHDGAFLAVCDASK-VVTVFSVAD-GYSENNVFYGHHAKIVCLAWSPDNEHFASGGMDMMV
KGPVTDV.YSHDGAFLAVCDAS..V.TVFSVAD.GYS...VFYGH.AKIVCLA..PDNEHFASG.MDMMV
RetrocopyKGPVTDVTYSHDGAFLAVCDASR<VITVFSVAD>GYS-SSVFYGHRAKIVCLA*FPDNEHFASGVMDMMV
ParentalYVWTLSDPETRVKIQDAHRLHHVSSLAWLDEHTLVTTSHDASVKEWTITY
Y.WTLSDPETRV.IQDAHRL.HVSSLAWLDEHTLVTTSHDASVK..TITY
RetrocopyYIWTLSDPETRVEIQDAHRLYHVSSLAWLDEHTLVTTSHDASVKD*TITY

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 .89 RPM 103 .79 RPM
SRP051959_heart 1 .03 RPM 67 .72 RPM
SRP051959_kidney 2 .31 RPM 76 .74 RPM
SRP051959_liver 1 .34 RPM 32 .73 RPM
SRP051959_lung 2 .42 RPM 59 .99 RPM
SRP051959_lymph_node 1 .83 RPM 86 .82 RPM
SRP051959_skeletal_muscle 0 .83 RPM 59 .44 RPM
SRP051959_spleen 1 .34 RPM 64 .52 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_1046 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1046 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1046 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000011293 2 retrocopies
retro_cjac_1046 , retro_cjac_3932,


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