RetrogeneDB ID:

retro_cjac_1566

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:17:63166982..63167540(+)
Located in intron of:ENSCJAG00000011778
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IFT27
Ensembl ID:ENSCJAG00000013961
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1566
ATGGTGAAGCTGGCAGCCAAATGCATCCTGGCAGGAGACCCAGCAGTGGGCAAGAGCACCCTGGCCCAGATCTTCCACAG
TGACGGAGCCCATTTCCAGAAGAGCTATACACTGACAACAGGAATGGATTTGGTGGTAAAGACAGTGCCAGTTCCTGACA
CAGGAGACAGTGTGGAACTCTTCATTTTTGACTCTGCTGGCAAGGAGCTGTTTTCGGAAATGCTGGATAAATTGTGGGAG
AGTCCCAACGTCTTCTGTCTCGTCTATGATGTGACCAATGAACAGTGCTTCAACAACTGCAGCAAGTGGCTGGAGAAGGC
TCGGTCACAGGCTCCAGGCATCTGTCTCCCACGTGTTTTAGTTGGGAACAAGACAGACCTGGTCAGCAGACAATAAGTGG
ACTCCGCTGAGGCCCGGGCGTGGGCGCTGGGCCAGGGCCTTGAATGCTTTGAAACATCCCTGAAGGAGATGGAAAACTTT
GAAGGCCCTTTCCACTGCCTGGACAAGCATTTCCAACAGCTGTACCGGGAGAAGATGGAGGTTTTCTGGGCACTGGTG

ORF - retro_cjac_1566 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.48 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVKLAAKCILAGDPAVGKTALAQIFCSDGAHFQKSYTLTTGIDLVVKTVPVPDTGDSVEFFIFDSAGKEL
MVKLAAKCILAGDPAVGK..LAQIF.SDGAHFQKSYTLTTG.DLVVKTVPVPDTGDSVE.FIFDSAGKEL
RetrocopyMVKLAAKCILAGDPAVGKSTLAQIFHSDGAHFQKSYTLTTGMDLVVKTVPVPDTGDSVELFIFDSAGKEL
ParentalFSEMLDKLWENPNVLCLVYDVTSEQSFSNCSKWLEKARSQAPGICLPGVLVGNKTDLASRQAVDSTEARA
FSEMLDKLWE.PNV.CLVYDVT.EQ.F.NCSKWLEKARSQAPGICLP.VLVGNKTDL.SRQ.VDS.EARA
RetrocopyFSEMLDKLWESPNVFCLVYDVTNEQCFNNCSKWLEKARSQAPGICLPRVLVGNKTDLVSRQ*VDSAEARA
ParentalWALGQGLEFFETSVKELEDFKAPFHCLAEQFHQLYREKLKVFQALV
WALGQGLE.FETS.KE.E.F..PFHCL...F.QLYREK..VF.ALV
RetrocopyWALGQGLECFETSLKEMENFEGPFHCLDKHFQQLYREKMEVFWALV

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 0 .80 RPM 1 .24 RPM
SRP051959_heart 0 .51 RPM 2 .33 RPM
SRP051959_kidney 0 .53 RPM 2 .35 RPM
SRP051959_liver 0 .32 RPM 1 .82 RPM
SRP051959_lung 1 .01 RPM 2 .59 RPM
SRP051959_lymph_node 0 .98 RPM 1 .23 RPM
SRP051959_skeletal_muscle 0 .15 RPM 3 .58 RPM
SRP051959_spleen 0 .99 RPM 2 .29 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1566 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1566 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1566 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000266571 retrocopy
Callithrix jacchus ENSCJAG00000013961 1 retrocopy
retro_cjac_1566 ,



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