HsaINT0038393 @ hg19
Intron Retention
Gene
ENSG00000108821 | COL1A1
Description
collagen, type I, alpha 1 [Source:HGNC Symbol;Acc:2197]
Coordinates
chr17:48267904-48268285:-
Coord C1 exon
chr17:48268178-48268285
Coord A exon
chr17:48267958-48268177
Coord C2 exon
chr17:48267904-48267957
Length
220 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CTCTTGTCCCTTGCTCTCAGGGT
3' ss Score
10.31
Exon sequences
Seq C1 exon
GGTGATGCTGGTCCCAAAGGTGCTGATGGCTCTCCTGGCAAAGATGGCGTCCGTGGTCTGACTGGCCCCATTGGTCCTCCTGGCCCTGCTGGTGCCCCTGGTGACAAG
Seq A exon
GTGAGGTGGCCGCCTCCCCACCTTCTGCCCTAACACATAGCCTCCTCAGCAGGCCTGGGCACGGTTCCGTGGGGTTGCGTTGGGAGAGCAGGTCCTGCCAAACTGAGCTGTCAACCTGGGAACCTGGAGGGACCAGAAGGAGGGGAGGCTCTCCTGGGGTCATCTACTAGGAGTATTCAGGGGAGGCCCTGACCCTGAGCCTCTTGTCCCTTGCTCTCAG
Seq C2 exon
GGTGAAAGTGGTCCCAGCGGCCCTGCTGGTCCCACTGGAGCTCGTGGTGCCCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108821-COL1A1:NM_000088:33
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=PU(3.3=5.6)
A:
NA
C2:
PF0139113=Collagen=FE(28.3=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:
GTGATGCTGGTCCCAAAGGTG
R:
GCACCACGAGCTCCAGTG
Band lengths:
157-377
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)