Special

DmeINT0033629 @ dm6

Intron Retention

Gene
FBgn0030556 | mRNA-cap
Description
The gene mRNA-capping-enzyme is referred to in FlyBase by the symbol DmelmRNA-cap (CG1810, FBgn0030556). It is a protein_coding_gene from Dmel. It has 2 annotated transcripts and 2 polypeptides (1 unique). Gene sequence location is X:14240266..14242822. Its molecular function is described by: polynucleotide 5'-phosphatase activity; protein tyrosine phosphatase activity; protein tyrosine/serine/threonine phosphatase activity; mRNA guanylyltransferase activity. It is involved in the biological process described with: positive regulation of smoothened signaling pathway; 7-methylguanosine mRNA capping; dephosphorylation. 17 alleles are reported. The phenotypes of these alleles manifest in: wing; embryo. The phenotypic classes of alleles include: visible; female semi-sterile. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderately high expression. Peak expression observed within 00-18 hour embryonic stages. CAVEAT: These RNA-Seq temporal profiles depend upon RNA-Seq reads that are uniquely placed in the genome. For this reason, genes such as histones, Stellates and many classes of RNA genes that are present in multiple exact or near exact copies in the genome, expression levels may be reported as much lower than their true values.
Coordinates
chrX:14240588-14241125:-
Coord C1 exon
chrX:14240852-14241125
Coord A exon
chrX:14240785-14240851
Coord C2 exon
chrX:14240588-14240784
Length
67 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
CCATTCTCCGCCTCTGGCAGCTT
3' ss Score
6.88
Exon sequences
Seq C1 exon
GTCCCCGAATCCTGGGCATGAAGCATGGCATCATCAATCAGCGGCTGCAGGCGTTCAGTGTGCGCGGCAAGGACTTCTGGGACATTTGGATGTCTGCCCGGCTGCTGGGTGAGAAATTCTCGCGGACACTGGCACACGAACCGGATGGCCTCATCTTCCAGCCATCAAAGCAGCCCTACACGGCTGGCACATGCTCCGATGTCTTCAAATGGAAGCCACATGAGCTCAACTCGGTGGACTTTCGGCTGAAGATCATAACAGAGCGCGGCGAGGG
Seq A exon
GTGAGTTGTAGTGATCTATCCGTTCAACGGGCTCAATTCATACCATGCCATTCTCCGCCTCTGGCAG
Seq C2 exon
CTTGCTGACGAAAAAGGTGGGCTTCCTCTATGTCGGCGGACACGATGCACCCTATGGACGGATGCAAAGGTTAACGAAGGAGACCAGAGAATTGGACAACAGAATCGTTGAGTGCACCATGAATCAGTTTGGCAACTGGGACTTTATGCGCGAGCGAACGGACAAAAAGAATCCCAACAGTTATAATACAGCCCGCT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0030556:FBtr0073922:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.358
Domain overlap (PFAM):

C1:
PF0133114=mRNA_cap_enzyme=PD(37.2=77.2),PF0391910=mRNA_cap_C=PU(17.0=18.5)
A:
NA
C2:
PF0391910=mRNA_cap_C=FE(66.0=100)


Main Inclusion Isoform:
NA


Main Skipping Isoform:
FBpp0073739


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGATCATAACAGAGCGCGGC
R:
CTCGCGCATAAAGTCCCAGTT
Band lengths:
180-247
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Neural diversity
  • Neurogenesis
  • Neuronal activity
  • Splicing factor regulation (brain)
  • Splicing factor regulation (SL2)