RetrogeneDB ID:

retro_cjac_3542

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01183708.1:6494..6662(+)
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:ENSCJAG00000036789
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3542
GACTGCTTGAGCTCAGGAGTTTGAGACTATTCTGGACAACATAGTGAGACACCACCTCCACAAAAAAGTACAAAAATTAG
CTGGGCATAGTGGTGCACACCTATAGATCCAGCTACTTAGGAGTCTGAAGTAGGATGATCGCCTGAACCTGGGAGGTAAA
GGCTGCAG

ORF - retro_cjac_3542 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.14 %
Parental protein coverage: 94.64 %
Number of stop codons detected: 5
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalNCLNPGDRDHPGQHGETPTKK---KISWARWFTPVIPALWEAEVGGSPEPRRSRLQ
.CL..G..D..GQH.ETP......KISWA.W.TP..PA..E.EVG.SPEP.R.RLQ
RetrocopyDCLSSGV*DYSGQHSETPPPQKSTKISWA*WCTPIDPAT*ESEVG*SPEPGR*RLQ

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 .44 RPM 1 .11 RPM
SRP051959_heart 0 .32 RPM 0 .63 RPM
SRP051959_kidney 0 .51 RPM 0 .73 RPM
SRP051959_liver 0 .19 RPM 0 .71 RPM
SRP051959_lung 0 .44 RPM 0 .85 RPM
SRP051959_lymph_node 0 .53 RPM 0 .87 RPM
SRP051959_skeletal_muscle 0 .20 RPM 0 .39 RPM
SRP051959_spleen 0 .46 RPM 0 .78 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3542 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3542 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3542 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 1 parental gene, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000036789 16 retrocopies



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