RetrogeneDB ID:

retro_cjac_2081

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:22:47748783..47749864(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000008364
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2081
AGAGCCCTTTGCTCCTCCCTCAGAATGAATGGAGACCAGAAATCAGATGTTTATGCCCAAGAAAAGCAGGATTTCGTTCA
GCACTTCTCCCAGATTGTTACGGTGCTGACTGAGGATGAGATGGGGCACCCAGAGACAGGAGATGCTATCATTCGGCTCA
AGGAGGTCCTGGAGTACAACGCCATTGGAGGCAAGTATCACCGGGGTTTGACGGTGCTCGTAGCGTTCCGGGAGCTGATG
GAGACAAGGAAACAGGATGCTGATAGTCTCCAGCGGGCCCTGACTGTGGGCTGGTGTGTGGAACTGCTGTAAGCTTTCTT
CCTGGTGACAGATAACACCATGGATTCATCCCTCACCCGCCGGGGACAGATCTGCTGGTATCGGAAGCCAGGTGTGGGTT
TGGATGCCATCAATGATGCTATCCTTCTGAAAGCATGTGTCTACCACCTGCTGAAGCTCTACTGCCGGAGCAGGCCCATC
ACCTGAACCTGATCGAGCTCTTCCTGCAGAGTTCCTATCAGACTGAGATTGGGCAGACCCTGGACCTCATCACAGCCCCT
CAGGACAATGTGGATCTCGGCAGATTCACTGAAAAGAGGTACAAATCCATTGTCAAGTACAAGACGGCTTTCTACTCCTT
CTACCTTCCTGTAGCTGCAGCCATGTACACGGCAGGAATTGATGGCGAGAAGGAGCATGCCAATGCCAAGAAGATCCTGC
TGGAGATGGGAGAGTTCTTTCAGATTCAGGATGATTACCTGGACCTCTTTGGGGACCCCAGTGTGACTGGCAAAGTTGGC
ACTGACATGCAGGACAACAAATGCAGCTGGCTGGTGGTCCAGTGTCTGCAACGGTCCACTCCGAAACAGTGCCAGATCCT
GAAGGAAAATTACGGGCAGAAGGAGGCTGAGAAGGTGGCCAGAGTGAAGGCATTATAGGAGGAGCTGGATCTGCCGGCCA
CATTCTCGAAGTATGAGGAAGACAGTTACAACCACATTATGGCTCTCATTGAACAGTACAAAGCGCCCTGCCCCCAGCTA
TCTTTCTGGGGCTTGTGTGCAAAATCTACAAGCGGAAAAAG

ORF - retro_cjac_2081 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.84 %
Parental protein coverage: 86.16 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalRALCSSLRMNGDQKSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPETGDAIARLKEVLEYNAIGGKYHRGL
RALCSSLRMNGDQKSDVYAQEKQDFVQHFSQIV.VLTEDEMGHPETGDAI.RLKEVLEYNAIGGKYHRGL
RetrocopyRALCSSLRMNGDQKSDVYAQEKQDFVQHFSQIVTVLTEDEMGHPETGDAIIRLKEVLEYNAIGGKYHRGL
ParentalTVLVAFRELAEPRKQDADSLQRALTVGWCVELLQAFFLVTDDIMDSSLTRRGQICWYQKPGVGLDAINDA
TVLVAFREL.E.RKQDADSLQRALTVGWCVELL.AFFLVTD..MDSSLTRRGQICWY.KPGVGLDAINDA
RetrocopyTVLVAFRELMETRKQDADSLQRALTVGWCVELL*AFFLVTDNTMDSSLTRRGQICWYRKPGVGLDAINDA
ParentalVLLEACVYRLLKLYCR-EQPYYLNLIELFLQSSYQTEIGQTLDLITAPQDNVDLDRFTEKRYKSIVKYKT
.LL.ACVY.LLKLYCR.EQ...LNLIELFLQSSYQTEIGQTLDLITAPQDNVDL.RFTEKRYKSIVKYKT
RetrocopyILLKACVYHLLKLYCR<EQAHHLNLIELFLQSSYQTEIGQTLDLITAPQDNVDLGRFTEKRYKSIVKYKT
ParentalAFYSFYLPVAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKVGTDIQDNKCSWLV
AFYSFYLPVAAAMY.AGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKVGTD.QDNKCSWLV
RetrocopyAFYSFYLPVAAAMYTAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKVGTDMQDNKCSWLV
ParentalVQCLQRSTPEQRQILKENYGQKEAEKVARVKALYEELDLPAVFSKYEEDSYNHIMALIEQYAAP-LPPAI
VQCLQRSTP.Q.QILKENYGQKEAEKVARVKAL.EELDLPA.FSKYEEDSYNHIMALIEQY.AP.LPPAI
RetrocopyVQCLQRSTPKQCQILKENYGQKEAEKVARVKAL*EELDLPATFSKYEEDSYNHIMALIEQYKAP<LPPAI
ParentalFLGLARKIYKRKK
FLGL..KIYKRKK
RetrocopyFLGLVCKIYKRKK

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 23 .47 RPM
SRP051959_heart 0 .00 RPM 5 .24 RPM
SRP051959_kidney 0 .00 RPM 7 .57 RPM
SRP051959_liver 0 .02 RPM 106 .46 RPM
SRP051959_lung 0 .00 RPM 8 .85 RPM
SRP051959_lymph_node 0 .00 RPM 11 .07 RPM
SRP051959_skeletal_muscle 0 .00 RPM 5 .57 RPM
SRP051959_spleen 0 .00 RPM 6 .70 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2081 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2081 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2081 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 13 parental genes, and 57 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000307492 retrocopies
Callithrix jacchus ENSCJAG00000008364 11 retrocopies
Echinops telfairi ENSETEG000000011546 retrocopies
Homo sapiens ENSG000001607526 retrocopies
Microcebus murinus ENSMICG000000074681 retrocopy
Macaca mulatta ENSMMUG000000231443 retrocopies
Mus musculus ENSMUSG000000597435 retrocopies
Nomascus leucogenys ENSNLEG000000120996 retrocopies
Pongo abelii ENSPPYG000000007473 retrocopies
Pan troglodytes ENSPTRG000000014229 retrocopies
Rattus norvegicus ENSRNOG000000433773 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000044751 retrocopy
Tursiops truncatus ENSTTRG000000133261 retrocopy



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