HsaINT0038383 @ hg19
Intron Retention
Gene
ENSG00000108821 | COL1A1
Description
collagen, type I, alpha 1 [Source:HGNC Symbol;Acc:2197]
Coordinates
chr17:48271304-48271544:-
Coord C1 exon
chr17:48271491-48271544
Coord A exon
chr17:48271403-48271490
Coord C2 exon
chr17:48271304-48271402
Length
88 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
TTCGTGCCTCCCATCCTTAGGGT
3' ss Score
10.84
Exon sequences
Seq C1 exon
GGTCTGACTGGAAGCCCTGGCAGCCCTGGTCCTGATGGCAAAACTGGCCCCCCT
Seq A exon
GTAAGTATCACTCCCCCTGAACCCCCTGCCATTGTCCTGTCTGCCTCCCTGCTGTCCTCACTGCTGCTTTCGTGCCTCCCATCCTTAG
Seq C2 exon
GGTCCCGCCGGTCAAGATGGTCGCCCCGGACCCCCAGGCCCACCTGGTGCCCGTGGTCAGGCTGGTGTGATGGGATTCCCTGGACCTAAAGGTGCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108821-COL1A1:NM_000088:24
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(19.5=100)
A:
NA
C2:
PF0139113=Collagen=FE(36.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCTGACTGGAAGCCCTGG
R:
CCTTTAGGTCCAGGGAATCCC
Band lengths:
146-234
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)