HsaINT0038891 @ hg19
Intron Retention
Gene
ENSG00000168542 | COL3A1
Description
collagen, type III, alpha 1 [Source:HGNC Symbol;Acc:2201]
Coordinates
chr2:189866123-189866315:+
Coord C1 exon
chr2:189866123-189866176
Coord A exon
chr2:189866177-189866261
Coord C2 exon
chr2:189866262-189866315
Length
85 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACC
5' ss Score
9.24
3' ss Seq
CATGGCTTCTCTTTTTCCAGGGT
3' ss Score
10.26
Exon sequences
Seq C1 exon
GGTCCTACTGGTCCTATTGGTCCTCCTGGCCCAGCTGGCCAGCCTGGAGATAAG
Seq A exon
GTAACCCTTAATACTACCTGGATATAAAAAGAAAATGTCTCTCTCTTTTGGATGCAAGACAGTGACATGGCTTCTCTTTTTCCAG
Seq C2 exon
GGTGAAGGTGGTGCCCCCGGACTTCCAGGTATAGCTGGACCTCGTGGTAGCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168542-COL3A1:NM_000090:33
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=FE(25.4=100),PF0139113=Collagen=FE(26.6=100),PF0139113=Collagen=PU(3.1=11.1)
A:
NA
C2:
PF0139113=Collagen=PD(16.4=61.1),PF0139113=Collagen=FE(26.6=100),PF0139113=Collagen=FE(26.2=100),PF0139113=Collagen=PU(7.4=27.8)
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:
ACTGGTCCTATTGGTCCTCCTG
R:
CCACGAGGTCCAGCTATACCTG
Band lengths:
95-180
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)