RetrogeneDB ID:

retro_cjac_1182

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:14:5627666..5628086(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:COTL1
Ensembl ID:ENSCJAG00000004056
Aliases:None
Description:coactosin-like 1 (Dictyostelium) [Source:HGNC Symbol;Acc:18304]


Retrocopy-Parental alignment summary:






>retro_cjac_1182
ATAGCCACCAAGATCGACAAAGAAGCTTGCTGGGCGGCGTACAACCTGGTGCGCGACGACGGCTCGTCCGTCATCTGGGT
GACTTTTAAATATGACGGCTCCACCATCGTCCCCGGCGAGCAGGGAGCGGAATACCAGCACTTCATCCAGCAGTGCACAG
ATGACGTCCGGTTGTTTGCCTTCGTGCGCTTCACCACCGGGGATGCCATGAGCAAGAAGCCCAAGTTCACTCTCATCACA
TGGATCAGTGAGGACGTCAGCGGGCTGGAGCGCGCCAAAACCAGGACGGACAAGACCCTGGTCAAGGAGGTCGTATAGAA
TTTCGCTAAGGAGTTTGTGATCAGTGATCGGAAGGAGCTGGAGGAAGATTTCATCAAGAGTGAGCTGAATAAGGCGGGCG
GAGCCATCTACGACGCCCAG

ORF - retro_cjac_1182 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.43 %
Parental protein coverage: 98.59 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMATKIDKEACRAAYNLVRDDGSAVIWVTFKYDGSTIVPGEQGAEYQHFIQQCTDDVRLFAFVRFTTGDAM
.ATKIDKEAC.AAYNLVRDDGS.VIWVTFKYDGSTIVPGEQGAEYQHFIQQCTDDVRLFAFVRFTTGDAM
RetrocopyIATKIDKEACWAAYNLVRDDGSSVIWVTFKYDGSTIVPGEQGAEYQHFIQQCTDDVRLFAFVRFTTGDAM
ParentalSKRSKFALITWIGEDVSGLQRAKTGTDKTLVKEVVQNFAKEFVISDRKELEEDFIKSELKKAGGANYDAQ
SK..KF.LITWI.EDVSGL.RAKT.TDKTLVKEVV.NFAKEFVISDRKELEEDFIKSEL.KAGGA.YDAQ
RetrocopySKKPKFTLITWISEDVSGLERAKTRTDKTLVKEVV*NFAKEFVISDRKELEEDFIKSELNKAGGAIYDAQ

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 .02 RPM 16 .62 RPM
SRP051959_heart 0 .04 RPM 4 .79 RPM
SRP051959_kidney 0 .04 RPM 27 .87 RPM
SRP051959_liver 0 .02 RPM 8 .40 RPM
SRP051959_lung 0 .02 RPM 18 .02 RPM
SRP051959_lymph_node 0 .05 RPM 32 .88 RPM
SRP051959_skeletal_muscle 0 .00 RPM 1 .29 RPM
SRP051959_spleen 0 .06 RPM 28 .34 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1182 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1182 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1182 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000004056 4 retrocopies
Macaca mulatta ENSMMUG000000070391 retrocopy



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