RetrogeneDB ID:

retro_cjac_444

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:87213530..87215253(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MVP
Ensembl ID:ENSCJAG00000007166
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_444
GGCATCCAGGATGTGTACATGCTGTCAGAGCAGGAGGGGCTGCTGCTGAGGGCCCTGCAGCCCCTGGAGGACGGGGAGGA
TGTGGAGAAGGTCTCACGCCAGGCTGGGGACCACTGGCTCATCCGCGGACTCCTGGAGTACGTGCCATCTGCCAAGGTGG
AGGTGGTGGAGGAGCGCCAGGCCATCCCTCTAGATGAGAACGAGGGCATCTATGTGCAGGGTGTTGAGACGGGAAAGGTG
TGGGCCGTGATCGGAAGCACCTACATGCTGATGGAGGATGAAGTCCTGTGGGAGAAGGAGCTGCCTCCCGGGGTGGAGGA
GCTGCTCAACAAGGGGCAGGACCCCTCTGGCAGACAGGGGTGACAAGGGCACAGCTAAGAGCCTCCAGCCCTCCACGCCC
CGGAACAAGACCCATGTGGTCAGCTACCGCGTGCCCCACAACGCTGCCGTGCAGGTGTATGACTACCGAGCGAAGTGAGC
CCGTGTGGTCTTTGGGCCTGAGCTGGTGTCGCTGGGTCCTGAGGAGCATTTCATGGTGCTGTCCCTTTCGGCCGGGTGGC
CCAAGTGTCCCCATGCCCACCGTGCGCTCTGCCTGCTTCTTGGGCCTGACTTCTTCACAGACGTCACCACCATTGAAACA
GCGGATCATGCCAGGCTGCAACTGCAGCTGGCCTACAATTGGCACTTCGAGGTGAATGACCGGAAGGACCCCCAAGAGAC
AGCCAAGCTCTTTTCTGTGCCAGACTTTGTAGGTGACGCCTGCAAGGCCATCGCATCCTGGGTACGGGGAGGCTGTGGCC
TCTCACTTTCGATGATTTCCATAAGAACTCGGCCCGCATCATTCGCACTGCCGTCTTTGGCTTTGAGACCTCGGAAGCCA
AGGGCCCCGATGGCATAACCCTGCCCAGGCCCCGGGATCGGGCTGTCTTCTCCCAAAATGGGCTGGTGGTCAGGAGCATG
GATGTGTAGTCAGTAGAGCCCGTGGACCAGAGAACCCGGGACGCCCTGCAACGTAGTGTCTAGCTGGCCATTGAGATCAC
CACCAACTCCCAGGAAGCGGCAACCAAGCACGAGGCTCAGAGACTGGAGCAGGAAGCCCGCAGCCGACTTGAGCGGCAGA
AGATCCTGGACCAGTCAGAAGCTGAGAAATCGCGCAAGGAACTCTGGGAGCTGGAGGCTCTGAGCATGGCCGTGGAGAGC
ACCGGGAACGCCAAGGCAGAGGCTGAGTCCCGTGCAGAGGCAGCCCAGATTGAGGGAGAAGGATCCGTGCTGCAGGCCAA
TCTGAAAGCAGAGGCCTTGGCCATCGAGACGGAGGCTGAGCTCCCGCGGGTACAGAAGGTCCGAGAGCTGGAACTGGTTT
ATGCCTGGGCCCAGCTGGAGCTGGAGGTGAGCAAGGCTCAGCAGCTGTCTGAGGTGGAGGTGAAGAAGTTCAAGCAGATG
ACAGAGGCTCTGGGCCCCAGCACCATCAGGGACCTTGCTATGGCTGGGCCTGAGATGCAGGTCAAACTGCTCCAGTCCCT
GGGCCTGAAATCAACCCTGATCACTGATGGTTCCACTCCCATCAATCTCTTCAACACGGCTTTGGGCTGCTGGGGATGGG
GCCTGAGGGTCAGCCCCTGGGCAAAGGGTGGTCAGTGGGCCCAGCCCCGGGGAGGGCATATCCCTTCAGTCTGCTCAGAC
CCCCAAAGCTCCTGCAGACAACCACGTGGTGCCTGTACTGCAC

ORF - retro_cjac_444 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.88 %
Parental protein coverage: 64.39 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalGIQDVYVLSEQEGLLLRALQPLEEGEDVEKVSRQAGDHWLIRGPLEYVPSAKVEVVEERQAIPLDENEGI
GIQDVY.LSEQEGLLLRALQPLE.GEDVEKVSRQAGDHWLIRG.LEYVPSAKVEVVEERQAIPLDENEGI
RetrocopyGIQDVYMLSEQEGLLLRALQPLEDGEDVEKVSRQAGDHWLIRGLLEYVPSAKVEVVEERQAIPLDENEGI
ParentalYVQDVKTGKVRAVIGSTYMLTEDEVLWEKELPPGVEELLNKGQDP-LADRGDKGTAKSLQPSAPRNKTRV
YVQ.V.TGKV.AVIGSTYML.EDEVLWEKELPPGVEELLNKGQDP.LADRGDKGTAKSLQPS.PRNKT.V
RetrocopyYVQGVETGKVWAVIGSTYMLMEDEVLWEKELPPGVEELLNKGQDP>LADRGDKGTAKSLQPSTPRNKTHV
ParentalVSYRVPHNAAVQVYDYRAKRARVVFGPELVSLGPEEQFTVLSLSAGRPKRPHARRALCLLLGPDFFTDVI
VSYRVPHNAAVQVYDYRAK.ARVVFGPELVSLGPEE.F.VLSLSAG.PK.PHA.RALCLLLGPDFFTDV.
RetrocopyVSYRVPHNAAVQVYDYRAK*ARVVFGPELVSLGPEEHFMVLSLSAGWPKCPHAHRALCLLLGPDFFTDVT
ParentalTIETADHARLQLQLAYNWHFEVNDRKDPQETAKLFSVPDFVGDACKAIASRVRGAVA-SVAFDDFHKNSA
TIETADHARLQLQLAYNWHFEVNDRKDPQETAKLFSVPDFVGDACKAIAS.VRG.......FDDFHKNSA
RetrocopyTIETADHARLQLQLAYNWHFEVNDRKDPQETAKLFSVPDFVGDACKAIASWVRGGCG<PLTFDDFHKNSA
ParentalRIIRTAVFGFETSEAKGPDGIALPRPRDRAVFPQNGLVVSSVDVQSVEPVDQRTQDALQRSVQLAIEITT
RIIRTAVFGFETSEAKGPDGI.LPRPRDRAVF.QNGLVV.S.DV.SVEPVDQRT.DALQRSV.LAIEITT
RetrocopyRIIRTAVFGFETSEAKGPDGITLPRPRDRAVFSQNGLVVRSMDV*SVEPVDQRTRDALQRSV*LAIEITT
ParentalNSQEAAAKHEAQRLEQEARGRLERQKILDQSEAEKARKELLELEALSMAVESTGNAKAEAESRAEAARIE
NSQEAA.KHEAQRLEQEAR.RLERQKILDQSEAEK.RKEL.ELEALSMAVESTGNAKAEAESRAEAA.IE
RetrocopyNSQEAATKHEAQRLEQEARSRLERQKILDQSEAEKSRKELWELEALSMAVESTGNAKAEAESRAEAAQIE
ParentalGEGSVLQAKLKAEALAIETEAELQRVRKVRELELVYARAQLELEVSKAQQLAEVEVKKFKQMTEALGPST
GEGSVLQA.LKAEALAIETEAEL.RV.KVRELELVYA.AQLELEVSKAQQL.EVEVKKFKQMTEALGPST
RetrocopyGEGSVLQANLKAEALAIETEAELPRVQKVRELELVYAWAQLELEVSKAQQLSEVEVKKFKQMTEALGPST
ParentalIRDLAVAGPEMQVKLLQSLGLKSTLITDGSTPINLFNTA-FGLLGMGPEGQPLGR-RVVSGPSPGEGISL
IRDLA.AGPEMQVKLLQSLGLKSTLITDGSTPINLFNTA.FGLLGMGPEGQPLG..RVVSGPSPGEGISL
RetrocopyIRDLAMAGPEMQVKLLQSLGLKSTLITDGSTPINLFNTA<FGLLGMGPEGQPLGK<RVVSGPSPGEGISL
ParentalQSAQAPKAPADNHVVPVLH
QSAQ.PKAPADNHVVPVLH
RetrocopyQSAQTPKAPADNHVVPVLH

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 .09 RPM 193 .65 RPM
SRP051959_heart 0 .00 RPM 22 .00 RPM
SRP051959_kidney 0 .11 RPM 54 .27 RPM
SRP051959_liver 0 .02 RPM 17 .42 RPM
SRP051959_lung 0 .00 RPM 34 .83 RPM
SRP051959_lymph_node 0 .09 RPM 43 .35 RPM
SRP051959_skeletal_muscle 0 .07 RPM 18 .45 RPM
SRP051959_spleen 0 .04 RPM 37 .04 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_444 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_444 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_444 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 ENSCJAG00000007166 1 retrocopy
retro_cjac_444 ,


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