HsaINT0038839 @ hg19
Intron Retention
Gene
ENSG00000139219 | COL2A1
Description
collagen, type II, alpha 1 [Source:HGNC Symbol;Acc:2200]
Coordinates
chr12:48375559-48375943:-
Coord C1 exon
chr12:48375890-48375943
Coord A exon
chr12:48375613-48375889
Coord C2 exon
chr12:48375559-48375612
Length
277 bp
Sequences
Splice sites
5' ss Seq
CGAGTAAGT
5' ss Score
10.15
3' ss Seq
TCTACCTGCTCTCCCCGCAGGGC
3' ss Score
13.53
Exon sequences
Seq C1 exon
GGTGACGTTGGTGAGAAAGGCCCTGAGGGAGCCCCTGGAAAGGATGGTGGACGA
Seq A exon
GTAAGTGAATGCGGGCTGCTGGACTGCTGGGCATTAGGATCCTAGCCCTGCACCCAGGAGAGCAGGAGAGAGGGCTGGGCAGTCTGCCACTGGGGTCCCTGGTCCTGTCTCTGTCGGGGCTGGGCAACTGCAGGGACTTCTCTGTTAAAATGGGGCCAGAGGGTAAGTGGGAGCTCTGGAGGCGGTGGGAGCACGCACCAAGGTTGGCTTGGTGCCGGGCCGCACGTGCTCGGCTGGCTCAGCCTGCCTCCCTCACCTCTACCTGCTCTCCCCGCAG
Seq C2 exon
GGCCTGACAGGTCCCATTGGCCCCCCTGGCCCAGCTGGTGCTAATGGCGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139219-COL2A1:NM_001844:35
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.950 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(23.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(23.9=100),PF0139113=Collagen=PU(15.9=61.1)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)