HsaINT0038882 @ hg19
Intron Retention
Gene
ENSG00000168542 | COL3A1
Description
collagen, type III, alpha 1 [Source:HGNC Symbol;Acc:2201]
Coordinates
chr2:189861891-189862115:+
Coord C1 exon
chr2:189861891-189861944
Coord A exon
chr2:189861945-189862061
Coord C2 exon
chr2:189862062-189862115
Length
117 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGT
5' ss Score
10.65
3' ss Seq
CTAACTGTTCTTGTTTTTAGGGT
3' ss Score
10.99
Exon sequences
Seq C1 exon
GGTGCTCCTGGTAAGAATGGAGAACGAGGTGGCCCTGGAGGACCTGGCCCTCAG
Seq A exon
GTACGTAGCTTTCCTCAATTTATTTCTAGCCTTCTAATAGATGCGTTCATCTCCAACCTTCTGACTTCTCTCTGTAATCTGTATTATTTCTACTTCCCTAACTGTTCTTGTTTTTAG
Seq C2 exon
GGTCCTCCTGGAAAGAATGGTGAAACTGGACCTCAGGGACCCCCAGGGCCTACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168542-COL3A1:NM_000090:25
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(8.2=27.8),PF0139113=Collagen=PU(23.4=83.3)
A:
NA
C2:
PF0139113=Collagen=FE(26.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGCTCCTGGTAAGAATGGA
R:
CTGGGGGTCCCTGAGGTC
Band lengths:
100-217
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)