RetrogeneDB ID:

retro_cjac_1917

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:65484350..65485591(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MKNK2
Ensembl ID:ENSCJAG00000000539
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1917
CAGCCAGCCCATTGACATCCCGGACGCCAAGAAGAGGGGCAAGAAGAAGAAGCGCGGCCGGGCCACCAACAGCTTCTTGG
GCAGGTTTGAAGACATCCACTGGCTACGGGAGGATGTTCTGGGTGAGGGCGCCCATGCCCACCTGCAGACCTGCATCAAC
CTGATCACCAGCCAGGATTACGCTGTCAAGATCATTGAGAAGCAGCCAGGCCACATTCGGAGCAGGGTTTTCCGGGAGGT
GGAGATGCTGTACCAGTGCCAGGGACACAGGAACGTTCTAGAGCTGATTGAGTTCTTCGAGGAGGAGGACCGCTTCTACC
TGGTATTTGAGAAGATGCAGGAGGCTCCATCCTGAGCCACAACCACAAGCGCCGGCACTTCAACGAGCTGGAGGCCAGTG
TGGTGGTGCAGGACGTGGCCAGTGCCTTGGACTTTTTGCACAACAAAGGCATCACCCACAGGGACCTAAAGCCGAAAAAC
ATCCTCTGTGAGCACCCCAACGGGGTCTTCCCCGTGAAGATCTGTGACTTCTACCTGGGCAGCGGCATCAAACTCAACAG
GGACTGCTCCCCCATCTCCACCCCGGAGCTGCTCACCCTGTGCGGCTCGGCGGAGTACATGGCCCCGGAGGTGGTGGAGG
TCTTCAGCAAGGAGGCCAACATCTACAACAAGTGCTGCGACCTGTGGAGCCTGATCGTCATCCTGTACATCCTGCTCAGC
GGCTACCCACCCTTTGTGGGCTGCTGCGGCGGCAACTGAGGCTGGTTCCACGGCGAGGCCTGCACTGCCTGCCAGAACAT
GCTGTTTGAGAGCATCCAGGAGGGCAAGTACGAGTTTCCCGACAAGGACTGGGCCCACATCTCCTGCGCCACCAAAGACC
TCATCTCCAAGCTGCTTGTCTGCGACTCCAAGCAGAGGCTGAGCGCTGCCCAAGTCCTGCAACATCCCTGGGTTCAAGGG
TGTGCCCCGGAGAACACTCTGCCCACTCCCATGGTCCTGCAGAGGAACAGCTGTGCCAAAGACCTCACGTCCTTCGCAGC
AGAGCTCATCGCCATGAATCGGCAGCTGGCCCAGCGCGACGAGGACCTGGTGGAGGAGGAGGCTGCGGGGCAGGGCCAGC
CTGTCCTGGTCCGAGCTACCTCATGCTGCCTGCAGCTGTCACCGCCTCTGAGTCCAAGCTGGCCCAGCGGCAGCAAAGGG
CCAGCCTGTCCTCGGCCCCCGCGGTGTTGGTGGGAGACCGC

ORF - retro_cjac_1917 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.45 %
Parental protein coverage: 89.59 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalQPAHRHP-DAKKRGKKKKRGRATDSFSGRFEDVYQLQEDVLGEGAHARVQ-CINLITSQEYAVKIIEKQP
QPAH.HP.DAKKRGKKKKRGRAT.SF.GRFED...L.EDVLGEGAHA..Q.CINLITSQ.YAVKIIEKQP
RetrocopyQPAH*HP>DAKKRGKKKKRGRATNSFLGRFEDIHWLREDVLGEGAHAHLQTCINLITSQDYAVKIIEKQP
ParentalGHIRSRVFREVEMLYQCQGHRNVLELIEFFEEEDRFYLVFEKMR-GGSILSHIHKRRHFNELEASVVVQD
GHIRSRVFREVEMLYQCQGHRNVLELIEFFEEEDRFYLVFEKM..GGSILSH.HKRRHFNELEASVVVQD
RetrocopyGHIRSRVFREVEMLYQCQGHRNVLELIEFFEEEDRFYLVFEKMQ<GGSILSHNHKRRHFNELEASVVVQD
ParentalVASALDFLHNKGIAHRDLKPENILCEHPNQVSPVKICDFDLGSGIKLNGDCSPISTPELLTPCGSAEYMA
VASALDFLHNKGI.HRDLKP.NILCEHPN.V.PVKICDF.LGSGIKLN.DCSPISTPELLT.CGSAEYMA
RetrocopyVASALDFLHNKGITHRDLKPKNILCEHPNGVFPVKICDFYLGSGIKLNRDCSPISTPELLTLCGSAEYMA
ParentalPEVVEAFSEEASIYDKRCDLWSLGVILYILLSGYPPFVGRCGSDCGWDRGEACPACQNMLFESIQEGKYE
PEVVE.FS.EA.IY.K.CDLWSL.VILYILLSGYPPFVG.CG...GW..GEAC.ACQNMLFESIQEGKYE
RetrocopyPEVVEVFSKEANIYNKCCDLWSLIVILYILLSGYPPFVGCCGGN*GWFHGEACTACQNMLFESIQEGKYE
ParentalFPDKDWAHISCAAKDLISKLLVRDAKQRLSAAQVLQHPWVQGCAPENTLPTPMVLQRNSCAKDLTSFAAE
FPDKDWAHISCA.KDLISKLLV.D.KQRLSAAQVLQHPWVQGCAPENTLPTPMVLQRNSCAKDLTSFAAE
RetrocopyFPDKDWAHISCATKDLISKLLVCDSKQRLSAAQVLQHPWVQGCAPENTLPTPMVLQRNSCAKDLTSFAAE
ParentalAIAMNRQLAQRDEDLAEEEAAGQGQPVLVRATSRCLQLSPP-SESKLAQRRQRASLSSAPVVLVGDR
.IAMNRQLAQRDEDL.EEEAAGQGQPVLVRATS.CLQLSPP.SESKLAQR.QRASLSSAP.VLVGDR
RetrocopyLIAMNRQLAQRDEDLVEEEAAGQGQPVLVRATSCCLQLSPP<SESKLAQRQQRASLSSAPAVLVGDR

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 .13 RPM 11 .23 RPM
SRP051959_heart 0 .28 RPM 23 .47 RPM
SRP051959_kidney 0 .24 RPM 32 .84 RPM
SRP051959_liver 0 .43 RPM 27 .90 RPM
SRP051959_lung 0 .29 RPM 25 .80 RPM
SRP051959_lymph_node 0 .34 RPM 25 .00 RPM
SRP051959_skeletal_muscle 0 .55 RPM 62 .78 RPM
SRP051959_spleen 0 .17 RPM 28 .15 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_1917 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1917 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1917 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 ENSCJAG00000000539 1 retrocopy
retro_cjac_1917 ,


Copyright © RetrogeneDB 2014-2017