RetrogeneDB ID:

retro_cjac_3770

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01200013.1:204..602(+)
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:ENSCJAG00000020022
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3770
GTAATTTTTGTATTATCAGTAGAGATGGGTTTCTCCATGTTGGTCAGGCTGGTCTGGAACTCCTGACCCCAGATGATCTT
CCTGCCTCAGCCTCCCAAAATGCTGGGATTATAGGCATGAGCCACTGCACCCAGCGATTATTATTATTATTATTATTGTT
GTTGTTGAGACAGAGTCTCACTCTGTCACCCAGGCTGGAGTGCAGTGATGCGATCTCAGCTCACTGCAACCTCCGCCGCC
TGCATTCAAGCAATTCTCCTTCCTCAGCCTCCCGAGTAGCTGGGATCACAGGCGTGTGCCACCATGCTCAGCTAATGTTT
GTATTTTTAGGAGAGACAGGGTTTTGCCGTATTGGTGAGACTGGTCTCAAACTGCTGACCTCAGGTAATCCATCCGCC

ORF - retro_cjac_3770 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.97 %
Parental protein coverage: 91.39 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLIFVFLVET-GFLHVGQAGLKLFTSGDLPASASQSAVITGVSHCAWPSESNIILLFCFVLFFLRWSFTL-
.IFV..VE..GFLHVGQAGL.L.T..DLPASASQ.A.I.G.SHC.........LL....L..LR.S.TL.
RetrocopyVIFVLSVEM<GFLHVGQAGLELLTPDDLPASASQNAGIIGMSHCT----QRLLLLLLLLL--LRQSLTL<
ParentalVTQAGVQWCDLGSLQPPPPGFRQFSCLSLPSSWDYRHVPPCPA-FCIFI-EMEFYHVLQVGLELLTSGDP
VTQAGVQ.CDL.SLQPPPP.F.QFS.LSLPSSWD.R.VPPC.A..CIF..E..F......GL.LLTSG.P
RetrocopyVTQAGVQ*CDLSSLQPPPPAFKQFSFLSLPSSWDHRRVPPCSANVCIFR>ETGFCRIGETGLKLLTSGNP
ParentalPA
.A
RetrocopySA

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 .93 RPM
SRP051959_heart 0 .00 RPM 1 .19 RPM
SRP051959_kidney 0 .00 RPM 1 .18 RPM
SRP051959_liver 0 .00 RPM 0 .71 RPM
SRP051959_lung 0 .00 RPM 0 .67 RPM
SRP051959_lymph_node 0 .00 RPM 1 .10 RPM
SRP051959_skeletal_muscle 0 .00 RPM 0 .44 RPM
SRP051959_spleen 0 .00 RPM 0 .99 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3770 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3770 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3770 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 1 parental gene, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000020022 17 retrocopies



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