RetrogeneDB ID:

retro_cjac_1447

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:16:10250332..10251120(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000008652
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NECAP2
Ensembl ID:ENSCJAG00000008146
Aliases:None
Description:NECAP endocytosis associated 2 [Source:HGNC Symbol;Acc:25528]


Retrocopy-Parental alignment summary:






>retro_cjac_1447
ATGGAGGAGAGCGGGTACCAGTCGGTGCTGTGTGTCAAGCCTGACGTCCACGTCTACCGCATCCCTCCGCGGGCTACCAA
TCATGGCTACGGGGCCACGGAGTGGCAGCTGGATCAGCCGTCATGGAGTGGCCAGCTGAGGATCACTGCAAAGGGGCAGA
TGGCCTATATCAAGCTGGAGGACAGGACCTCAGGGGAGCTCTTTGCTCAGGCCCCAGTGGATCAGTTTCCTGGTACAGCT
GTGGAGAGCCTAACGGATTCCAGCAGGTACTTCGAGATCCGCATTGAAGATGGAAACGGGCGACGGGCATTTAATGGAAT
TGGCTTCGAGGACCGAGGTGATGCCTTTAACTTCCATGTTGCATTGCAGGATCGTTTCAAGTGGGTGAAACAGCAGTGCG
AATTTGCAAAACAAGCCCAGAACCCAGACCAAAGACCCAAATTGGACCTGGGCTTCAAGGAGGGCCAGACCATCAAGCTC
AATGTCGCAAACATGAAGAAGGAAGGAGCAGCCGGGAATCCCGAGCCCGGCCTGCCAGCACAGGAGGGTTGAGCTTGCTT
CCCCCTCCCCCAGAGGGCAAAACCACCACCCTCATCCGTCCCCCTGGGGAGCAGTTGTCGGTTGGGGGATCCCTCATCCA
GCCAGCAGTTACTCCCACTTCAGGAGGTGCTTCTGTACCCTGGCCATGGCCCGAGCCTGCCACCGCTGCCACTGCTGACA
TCTGGGGAGACTTTACCAAATCTACAGGATCAACTTCCAGCCAGACCCAACCAGGCTGGGTTCAGTTC

ORF - retro_cjac_1447 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.94 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMEESGYESVLCVKPDVHVYRIPPRATNRGYRAAEWQLDQPSWSGRLRITAKGQMAYIKLEDRTSGELFAQ
MEESGY.SVLCVKPDVHVYRIPPRATN.GY.A.EWQLDQPSWSG.LRITAKGQMAYIKLEDRTSGELFAQ
RetrocopyMEESGYQSVLCVKPDVHVYRIPPRATNHGYGATEWQLDQPSWSGQLRITAKGQMAYIKLEDRTSGELFAQ
ParentalAPVDQFPGTAVESVTDSSRYFVIRIEDGNGRRAFIGIGFGDRGDAFDFNVALQDHFKWVKQQCEFAKQAQ
APVDQFPGTAVES.TDSSRYF.IRIEDGNGRRAF.GIGF.DRGDAF.F.VALQD.FKWVKQQCEFAKQAQ
RetrocopyAPVDQFPGTAVESLTDSSRYFEIRIEDGNGRRAFNGIGFEDRGDAFNFHVALQDRFKWVKQQCEFAKQAQ
ParentalNPDQSPKLDLGFKEGQTIKLNIANMKKKEGAAGNP-RARPASTGGLSLLPPPPGGRTSTLIPPPGEQLSV
NPDQ.PKLDLGFKEGQTIKLN.ANM.KKEGAAGNP.RARPASTGGLSLLPPPP.G.T.TLI.PPGEQLSV
RetrocopyNPDQRPKLDLGFKEGQTIKLNVANM-KKEGAAGNP<RARPASTGGLSLLPPPPEGKTTTLIRPPGEQLSV
ParentalGGSLVQPAVAPTSGGASVPWPQPKPATAATADIWGDFTKSTGSTSSQTQPGWVQF
GGSL.QPAV.PTSGGASVPWP.P.PATAATADIWGDFTKSTGSTSSQTQPGWVQF
RetrocopyGGSLIQPAVTPTSGGASVPWPWPEPATAATADIWGDFTKSTGSTSSQTQPGWVQF

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 .00 RPM 12 .20 RPM
SRP051959_heart 0 .00 RPM 8 .61 RPM
SRP051959_kidney 0 .00 RPM 15 .51 RPM
SRP051959_liver 0 .00 RPM 9 .68 RPM
SRP051959_lung 0 .00 RPM 19 .07 RPM
SRP051959_lymph_node 0 .00 RPM 32 .94 RPM
SRP051959_skeletal_muscle 0 .00 RPM 4 .04 RPM
SRP051959_spleen 0 .00 RPM 34 .52 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1447 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1447 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1447 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000158951 retrocopy
Callithrix jacchus ENSCJAG00000008146 2 retrocopies
retro_cjac_1447 , retro_cjac_2449,
Macropus eugenii ENSMEUG000000061401 retrocopy



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