HsaINT0038873 @ hg19
Intron Retention
Gene
ENSG00000168542 | COL3A1
Description
collagen, type III, alpha 1 [Source:HGNC Symbol;Acc:2201]
Coordinates
chr2:189858764-189859058:+
Coord C1 exon
chr2:189858764-189858808
Coord A exon
chr2:189858809-189858959
Coord C2 exon
chr2:189858960-189859058
Length
151 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGC
5' ss Score
9.26
3' ss Seq
TGTCTTTGGTTTGTTCTTAGGGT
3' ss Score
10.09
Exon sequences
Seq C1 exon
GGCCCTCCTGGGATTAATGGTAGTCCTGGTGGTAAAGGCGAAATG
Seq A exon
GTAAGCTGTCCCCACTCCTCAGCCTTATCTCATCCACACATTACTGGCTTCTTTTGCATTTTGCATGACAATAGATTTGTGATATTTAAGTGAGATATTCATAAAAGAACATTCAAGTTCGGCTAATATAGTGTCTTTGGTTTGTTCTTAG
Seq C2 exon
GGTCCCGCTGGCATTCCTGGAGCTCCTGGACTGATGGGAGCCCGGGGTCCTCCAGGACCAGCCGGTGCTAATGGTGCTCCTGGACTGCGAGGTGGTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168542-COL3A1:NM_000090:17
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(10.7=37.5),PF0139113=Collagen=FE(25.9=100)
A:
NA
C2:
PF0139113=Collagen=PD(23.3=42.4),PF0139113=Collagen=PU(35.2=97.0)
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:
CCTCCTGGGATTAATGGTAGTCCT
R:
ACCACCTCGCAGTCCAGG
Band lengths:
138-289
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)