RetrogeneDB ID:

retro_cjac_1900

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:36464124..36464898(-)
Located in intron of:ENSCJAG00000016883
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NRM
Ensembl ID:ENSCJAG00000019904
Aliases:None
Description:nurim (nuclear envelope membrane protein) [Source:HGNC Symbol;Acc:8003]


Retrocopy-Parental alignment summary:






>retro_cjac_1900
ATGGCCCCTGCACTGCTCCTGGTCCCTGCTGCCCTCGCCTCTTTCATCCTAGCCTTTGGCACTGGAGTGGAGTTTACGCA
CTTTACCTCCCTTCAGTCACTTCTTGGAGGGATCCCAGAGTCTGGTGGTCCCAATGCCTGACAGGGATGGCTGGCTGCCC
TGCAGGACCGCAGCATCCTTGCCCCCCTGGCATGGGATCTGGGGCTCCTGCTTCTATTTGTTGGGCAGCACAGCCTCATA
GCAGCTGAGAGAGTGAAACCATGGCCATCCCGGTACTTTGGGGTCCTTCAGAGGTCACTGTATGTGGCCTGCACTGCCCT
GGCCTTGCAGCTGGTGATGCGGTACTGGGAGCCTGTACCCAGAGGCCCCGTGTTGTGGGAGGCTCGAGCTGAGCCATGGG
CCACCTGGGTGCCCCTCCTCTGCTTTGTGCTCCATATCATCTCCTGGCTCCTCATCTTCAGCATCCTTCTCGTCTTTGAC
TACACTGAGCTCATGGGCCTCAAACAGGTGTACTACCATGTGCTGGGGCTGGGCGAGCCTCTGGCCCTGAAGTCTCCCCG
GGCTCTCAGTCTCTTCTCCCACCTGCGCCACCCAGTGTGTGTGGAGCTGCTGACAGTGCTGTGGGTGGTGCCTACGCTTG
GCACAGACCATCTCCTCCTTACCCTCTACCTGGGCCTGGCTCATAGGCTTGATCAGCAAGACCTCTGCTACCTCCGGGCC
CAGCTGCAAAGAAAACTCCACCTGCTCTCTCGACCCCAGGATGGGGAGGCAGAG

ORF - retro_cjac_1900 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.98 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAPALLLVPAALASFILAFGTGVEFVRFASLQPLLGGIPESVGPDARQGWLAALQDRSILAPLAWDLGLL
MAPALLLVPAALASFILAFGTGVEF..F.SLQ.LLGGIPES.GP.A.QGWLAALQDRSILAPLAWDLGLL
RetrocopyMAPALLLVPAALASFILAFGTGVEFTHFTSLQSLLGGIPESGGPNA*QGWLAALQDRSILAPLAWDLGLL
ParentalLLFVGQHSLMAAERVKAWTSRYFGVLQRSLYVACTALALQLVMRYWEPIPRGPVLWEARAEPWATWVPLL
LLFVGQHSL.AAERVK.W.SRYFGVLQRSLYVACTALALQLVMRYWEP.PRGPVLWEARAEPWATWVPLL
RetrocopyLLFVGQHSLIAAERVKPWPSRYFGVLQRSLYVACTALALQLVMRYWEPVPRGPVLWEARAEPWATWVPLL
ParentalCFVLHVISWLLIFSILLVFDYAELMGLKQVYYHVLGLGEPLALKSPRALRLFSHLRHPVCVELLTVLWVV
CFVLH.ISWLLIFSILLVFDY.ELMGLKQVYYHVLGLGEPLALKSPRAL.LFSHLRHPVCVELLTVLWVV
RetrocopyCFVLHIISWLLIFSILLVFDYTELMGLKQVYYHVLGLGEPLALKSPRALSLFSHLRHPVCVELLTVLWVV
ParentalPTLGTDRLLLALLLTLYLGLAHGLDQQDLRYLRAQLQRKLHLLSRPQDGEAE
PTLGTD.LLL....TLYLGLAH.LDQQDL.YLRAQLQRKLHLLSRPQDGEAE
RetrocopyPTLGTDHLLL----TLYLGLAHRLDQQDLCYLRAQLQRKLHLLSRPQDGEAE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 2 .13 RPM 1 .24 RPM
SRP051959_heart 1 .61 RPM 2 .17 RPM
SRP051959_kidney 2 .17 RPM 1 .20 RPM
SRP051959_liver 1 .04 RPM 0 .80 RPM
SRP051959_lung 2 .20 RPM 3 .48 RPM
SRP051959_lymph_node 4 .00 RPM 2 .40 RPM
SRP051959_skeletal_muscle 1 .55 RPM 1 .35 RPM
SRP051959_spleen 1 .87 RPM 1 .97 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1900 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1900 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1900 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 ENSCJAG00000019904 1 retrocopy
retro_cjac_1900 ,



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