HsaINT0038415 @ hg19
Intron Retention
Gene
ENSG00000108821 | COL1A1
Description
collagen, type I, alpha 1 [Source:HGNC Symbol;Acc:2197]
Coordinates
chr17:48275093-48275363:-
Coord C1 exon
chr17:48275310-48275363
Coord A exon
chr17:48275147-48275309
Coord C2 exon
chr17:48275093-48275146
Length
163 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGC
5' ss Score
5.59
3' ss Seq
ACCTCTTCTATCTTTTCTAGGGT
3' ss Score
12.39
Exon sequences
Seq C1 exon
GGTCCCCAAGGCTTCCAAGGTCCCCCTGGTGAGCCTGGCGAGCCTGGAGCTTCA
Seq A exon
GTAAGCACTCTCTATACAGATTCATACTCCTTCTACAAACACACAGACTCTCCTATAGAAGAACTCCCAGGCCTGGGGTCTTCCTTACCTCTTCCCTTCAATCCCAGCCTTCCCCTTCTTTTTTTCTTATCCATATTCTAACCACCTCTTCTATCTTTTCTAG
Seq C2 exon
GGTCCCATGGGTCCCCGAGGTCCCCCAGGTCCCCCTGGAAAGAATGGAGATGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108821-COL1A1:NM_000088:8
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(27.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(27.4=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:
GGTCCCCAAGGCTTCCAAG
R:
CATCTCCATTCTTTCCAGGGGG
Band lengths:
106-269
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)