RetrogeneDB ID:

retro_cjac_3594

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01187181.1:3639..3917(-)
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:ENSCJAG00000035420
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3594
TTAGAGTGCAGTGACATGATCTTGGCTCACTGCAACCTCTGTCTCCTGGATTCCAGCAATACTCCCCTGCCTCAGCCTCC
TGAGTAGCTGGAATTACAGGTGCCCACCACCACACCGGGCTAATTTTTATACTTCTAGTAGAGATGGGGTGTTTCATCAC
ATTTCAGGCTGGTCTCGAGCTCATGACCTCAGGTAATCCACCCACCTCGGCCTCCCAAAGGGCTGGGATGACAGGCATGA
GCCACCATGTCTAGCCTGTGTATATATGTGTGTATATG

ORF - retro_cjac_3594 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.45 %
Parental protein coverage: 64.79 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLECSGAISAHCDLC-RPG-SNYSPASACRVAGITSTHHGTQLLFCTLVKMGFHHVGQAGLKLLTSADPPT
LECS..I.AHC.LC..PG...YSPASA..VAGIT..HH.T.L.F..LV.MG.....QAGL.L.TS..PPT
RetrocopyLECSDMILAHCNLC<SPGFQQYSPASAS*VAGITGAHHHTGLIFILLVEMGCFITFQAGLELMTSGNPPT
ParentalSASQMVGITGMSHCAQPFLYFVFL
SASQ..G.TGMSH...P....V..
RetrocopySASQRAGMTGMSHHV*PVYICVYM

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 0 .55 RPM
SRP051959_heart 0 .00 RPM 0 .40 RPM
SRP051959_kidney 0 .00 RPM 0 .51 RPM
SRP051959_liver 0 .00 RPM 0 .32 RPM
SRP051959_lung 0 .00 RPM 0 .60 RPM
SRP051959_lymph_node 0 .00 RPM 1 .10 RPM
SRP051959_skeletal_muscle 0 .00 RPM 0 .24 RPM
SRP051959_spleen 0 .00 RPM 0 .74 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3594 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3594 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3594 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 123 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG0000000815310 retrocopies
Callithrix jacchus ENSCJAG000000186761 retrocopy
Callithrix jacchus ENSCJAG000000315771 retrocopy
Callithrix jacchus ENSCJAG0000003182624 retrocopies
Callithrix jacchus ENSCJAG000000325722 retrocopies
Callithrix jacchus ENSCJAG000000330381 retrocopy
Callithrix jacchus ENSCJAG00000035420 16 retrocopies
Callithrix jacchus ENSCJAG0000003575834 retrocopies
Callithrix jacchus ENSCJAG0000003654213 retrocopies
Callithrix jacchus ENSCJAG0000003728816 retrocopies
Callithrix jacchus ENSCJAG000000379615 retrocopies



Copyright © RetrogeneDB 2014-2017