RetrogeneDB ID:

retro_cjac_1156

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:13:60087230..60088391(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:BBOX1
Ensembl ID:ENSCJAG00000006265
Aliases:None
Description:butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1 [Source:HGNC Symbol;Acc:964]


Retrocopy-Parental alignment summary:






>retro_cjac_1156
ATGGCTTGTACCATCCAAAAGGCAGAAGTGCTCGATGGGGCTCATTTGATGCAGATCCTCTGGAATGATGAGGCAGAGTC
TCTCTACCCAGCTGTATGCCTGCGAGACAACTGCCCATGCTCTGATTGCTACCTGGATTCTGCAAAAGCACGGAAACTTC
TCGTTGAAGCTCTTGATGTGAACATTGGAATTAAAGGCTTGACATTTGACAGAGAAAAGGTGTACATCACATGGCCCGAT
GAGCATTACAGTGAATTCCAGGCTGATTGGCTGAAGAAAAGATGCTTTTCCAAGCAGGCCAGAGCACAGCTCCAAAGAGA
ATTGTTTTTGCCAGAATGTCAGTACTGGGGCTCAGAGCTCCAGCTACCTACTCTGGATTTTGAAGATGTTTTACGATATG
ACAAACATGCATACAAGTGGCTCTCCACCCTCAAGAAAGTAGGCATAGTATGACTCACCGGAGCATCTGACAAACAAGGA
GAAGTTTTAAAACTTGGGAAAAGGATTGGTTTCCTCTATCTCACATTTTATGGACATACTGGGCAAGTGCAAGACAAAAT
CGATGCAAACAATGTGGCTTACACAACTGGGAAGCTAAGCTTTCATACTGATTATCCAGCCCTCCATCATCCACCTGGGG
TTCAGCTTCTTCACTGCATAAAGCAAACCGTCACAGGTGGTGATACAGAAATTGTAGATGGGTTTAATGTGTGCCAAAAG
TTAAAGAAAAAAAATCCTCAGGCATTCCAGATTTTGACCTCTACCTTTGTGGACTTTACAGACATTGGAGTGGATTACTG
TGATTTTTCTGTTCAATCAAAACACAAAATTATAGAGTTAGATGATAGAGGCCAAGTGGTTCGCATCAACTTCAATAACG
CAACTAGGGACACAATATTTGATGTGCCAGTTGAAAGAGTTCCGCCTTTTTATGCTGCTCTGAAGGAGTTCGTTGACCTC
ATGAACAGCAGAGAATCCAAGTTTACCTTCAAGATGAATCCAGGTGATGTGATTACTTTTGATAACTGGCGCTTACTTCA
TGGCCGACGTAGCTATGAAGCAGGAACTGAGATATCCCGCCATCTAGAAGGAGCTTATGCTGACTGGGATGTGGTCATGT
TAAGGCTTCGTCTCTTAAGGCAGAGGGTCAAGAATGGAAAC

ORF - retro_cjac_1156 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.93 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMACTIQKAEVLDGARLMQILWNDEAESLYPAVWLRDNCPCSDCYLDSAKARKLLVEALDVNIGIKGLTFD
MACTIQKAEVLDGA.LMQILWNDEAESLYPAV.LRDNCPCSDCYLDSAKARKLLVEALDVNIGIKGLTFD
RetrocopyMACTIQKAEVLDGAHLMQILWNDEAESLYPAVCLRDNCPCSDCYLDSAKARKLLVEALDVNIGIKGLTFD
ParentalREKVYITWPDEHYSEFQADWLKKRCFSKQARAQLQRELFLPECQYWGSELQLPTLDFEDVLRYDKHAYKW
REKVYITWPDEHYSEFQADWLKKRCFSKQARAQLQRELFLPECQYWGSELQLPTLDFEDVLRYDKHAYKW
RetrocopyREKVYITWPDEHYSEFQADWLKKRCFSKQARAQLQRELFLPECQYWGSELQLPTLDFEDVLRYDKHAYKW
ParentalLSTLKKVGIVRLTGASDKQGEVLKLGKRIGFLYLTFYGHTWQVQDKIDANNVAYTTGKLSFHTDYPALHH
LSTLKKVGIV.LTGASDKQGEVLKLGKRIGFLYLTFYGHT.QVQDKIDANNVAYTTGKLSFHTDYPALHH
RetrocopyLSTLKKVGIV*LTGASDKQGEVLKLGKRIGFLYLTFYGHTGQVQDKIDANNVAYTTGKLSFHTDYPALHH
ParentalPPGVQLLHCIKQTVTGGDTEIVDGFNVCQKLKKKNPQAFQILSSTFVDFTDIGVDYCDFSVQSKHKIIEL
PPGVQLLHCIKQTVTGGDTEIVDGFNVCQKLKKKNPQAFQIL.STFVDFTDIGVDYCDFSVQSKHKIIEL
RetrocopyPPGVQLLHCIKQTVTGGDTEIVDGFNVCQKLKKKNPQAFQILTSTFVDFTDIGVDYCDFSVQSKHKIIEL
ParentalDDRGQVVRINFNNATRDTIFDVPVERVQPFYAALKEFVDLMNSRESKFTFKMDPGDVITFDNWRLLHGRR
DDRGQVVRINFNNATRDTIFDVPVERV.PFYAALKEFVDLMNSRESKFTFKM.PGDVITFDNWRLLHGRR
RetrocopyDDRGQVVRINFNNATRDTIFDVPVERVPPFYAALKEFVDLMNSRESKFTFKMNPGDVITFDNWRLLHGRR
ParentalSYEAGTEISRHLEGAYADWDVVMSRLRLLRQRVKNGN
SYEAGTEISRHLEGAYADWDVVM.RLRLLRQRVKNGN
RetrocopySYEAGTEISRHLEGAYADWDVVMLRLRLLRQRVKNGN

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 0 .00 RPM
SRP051959_heart 0 .19 RPM 0 .07 RPM
SRP051959_kidney 0 .55 RPM 5 .13 RPM
SRP051959_liver 1 .13 RPM 12 .09 RPM
SRP051959_lung 0 .03 RPM 0 .03 RPM
SRP051959_lymph_node 0 .00 RPM 0 .00 RPM
SRP051959_skeletal_muscle 0 .00 RPM 0 .24 RPM
SRP051959_spleen 0 .04 RPM 0 .00 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_1156 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1156 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1156 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000006265 1 retrocopy
retro_cjac_1156 ,




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