RetrogeneDB ID:

retro_cjac_3932

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:GL286307.1:31445..32818(-)
Located in intron of:None
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_3932
GCTGGCCCGGGAGGCTTTTGGTGAGCATGAAGCAGTAGCAAGTGGGTGAGGACGTCGTACGAGATCAAGAAGGTGTTCAC
CAGCCTCCCCCAGGTGGAGAGGAGCATCTCCAAAATCATCAGCGGCGACCCTAAGGGCAACAATTTTCTGTATGCCAATG
GAAAGTGCGTCATCCTAAGGAACATCGACAACCCAGCCCTTGCTGACGTCTACACAGAGCACACCCATCAGGCGGTGGCG
GCAAAGTATTCGCCCAGCAGATTCTACATCGCCTCCGGAGATGTGTTTGGGAAGCTGAAGATCTAGGATACCACACAGAA
GGAGCACCTGTTGAAGTATGAATACCAGCCTTTCGCCAGGAACATCAAAGACATTGCCTGGACTGAAGACAGTAAGAGGA
TTGCCCTGGTCGGTGAAGGAAGGGAAAAGTTCGGAGCAGTCTTCCTGTGGGATAGTGGCTCTTCTGTGGGCGAAATCATG
GGCCACAACAAAGTCATCAACAGTGTGGACATTGAGCAAAGCCAGCCATACCGGTTGGCCACAGGAAGCGACAATAACTA
CACTATGTTCTTTGAGGGACCCCCATTCAAGTTCAAGTTCACAATTGGTGATCACAGCCGCTTTGTCAATTGTGTGTGAT
TCTCTCCTGATGGGAACAGATTTGCCACAGCCAGTGCCAAAGGCCAGATATACATCTGTGATGGGAAGACTGGGGAGAAG
GTGTGCACGCTGGGTGGAAGCAAGGCCCATGATGGTGGGATTTATGCCATTAGTTGGAGTCCTGACAACACCCATTTGCT
TTCTGCTTCCAGGGACAAAACTTCCAAGATCTGGGATGTTAACATAAACTTCGTGGTCAGCGTGTTTCCCATGGGCTCCA
TGGTTCTGGACCAGCAGCTGGGCTGACTGTGGCAGAAGGACCACCTGCTCAGTGTCTCCCTGTCCGGGTACATCAACTAT
CTGGACAGAACAACCCCAGCAAGCCCCTGCGTGTCATCAAGGGTCACAGTAAATCAATCCAGTGTCTGACAGTGCATAAA
AATGGCGGCAAGTCCTACATCTACTCTGGGAGCCATGATGGACACATTAATTACTGGGATTCAGAGACAAGGAAAAACGA
TTCCTTCGCTGGGAAGGGCCACATGAACCAGGTGTCCAGGATGACCATGGACAAGTTGGGGCAGCTCATCACCTGCAGCA
TGGATAACACTGAGCGGTACACCAACCTCACACTGTGGGACTACAGGGGACAAGGAGTAGTGGAACTGGACGTTCAGCCA
AAGTGTGTCACTGTGGGCCCTGGGGGATACACTGTGGTGCTGTGCATCGGGCAGATCATCCGGCTGAAAGATCAGAGGAA
GTGCTTAGCATTG

ORF - retro_cjac_3932 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.19 %
Parental protein coverage: 73.4 %
Number of stop codons detected: 5
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAGSGGFRRARRGNKWARMPYEIKKVFASLPQVERGVSKIIGGDPKGNNFLYTNGKCVILRNIDNPALADI
AG.GGF..A....KW.R..YEIKKVF.SLPQVER..SKII.GDPKGNNFLY.NGKCVILRNIDNPALAD.
RetrocopyAGPGGFW*A*SSSKWVRTSYEIKKVFTSLPQVERSISKIISGDPKGNNFLYANGKCVILRNIDNPALADV
ParentalYTEHAHQVVVARYSPSGFYIASGDVSGKLRIWDTTQKEHLLKYEYQPFAGKIKDIAWTEDSKRIAVVGEG
YTEH.HQ.V.A.YSPS.FYIASGDV.GKL.I.DTTQKEHLLKYEYQPFA..IKDIAWTEDSKRIA.VGEG
RetrocopyYTEHTHQAVAAKYSPSRFYIASGDVFGKLKI*DTTQKEHLLKYEYQPFARNIKDIAWTEDSKRIALVGEG
ParentalREKFGAVFLWDSGSSVGEITGHNKVINSVDIKQSRPYRLATGSDDNCAAFFEGPPFKFKFTIGDHSRFVN
REKFGAVFLWDSGSSVGEI.GHNKVINSVDI.QS.PYRLATGSD.N...FFEGPPFKFKFTIGDHSRFVN
RetrocopyREKFGAVFLWDSGSSVGEIMGHNKVINSVDIEQSQPYRLATGSDNNYTMFFEGPPFKFKFTIGDHSRFVN
ParentalCVRFSPDGNRFATASADGQIYIYDGKTGEKVCALGGSKAHDGGIYAXSWSPDSTHLLSASGDKTSKIWDV
CV.FSPDGNRFATASA.GQIYI.DGKTGEKVC.LGGSKAHDGGIYA.SWSPD.THLLSAS.DKTSKIWDV
RetrocopyCV*FSPDGNRFATASAKGQIYICDGKTGEKVCTLGGSKAHDGGIYAISWSPDNTHLLSASRDKTSKIWDV
ParentalNVNSVVSVFPMGTTVLDQQLGCLWQKDHLLSVSLSGYINYLDR-NNPSKPLRVIKGHSKSIQCLTVHKNG
N.N.VVSVFPMG..VLDQQLG.LWQKDHLLSVSLSGYINYLDR.NNPSKPLRVIKGHSKSIQCLTVHKNG
RetrocopyNINFVVSVFPMGSMVLDQQLG*LWQKDHLLSVSLSGYINYLDR<NNPSKPLRVIKGHSKSIQCLTVHKNG
ParentalGKSYIYSGSHDGHINYWDSETGENDSFAGKGHTNQVSRMTVDESGQLISCSMDDTVRYTNLTLRDYSGQA
GKSYIYSGSHDGHINYWDSET..NDSFAGKGH.NQVSRMT.D..GQLI.CSMD.T.RYTNLTL.DY.GQ.
RetrocopyGKSYIYSGSHDGHINYWDSETRKNDSFAGKGHMNQVSRMTMDKLGQLITCSMDNTERYTNLTLWDYRGQG
ParentalVVKLDVQPKCVAVGPGGYAVVVCIGQIVLLKDQRKCFSI
VV.LDVQPKCV.VGPGGY.VV.CIGQI..LKDQRKC...
RetrocopyVVELDVQPKCVTVGPGGYTVVLCIGQIIRLKDQRKCLAL

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 103 .79 RPM
SRP051959_heart 0 .00 RPM 67 .72 RPM
SRP051959_kidney 0 .02 RPM 76 .74 RPM
SRP051959_liver 0 .00 RPM 32 .73 RPM
SRP051959_lung 0 .00 RPM 59 .99 RPM
SRP051959_lymph_node 0 .00 RPM 86 .82 RPM
SRP051959_skeletal_muscle 0 .04 RPM 59 .44 RPM
SRP051959_spleen 0 .00 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_3932 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3932 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3932 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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