HsaALTD0001537-2/2 @ hg19
Alternative 5'ss
Gene
ENSG00000108821 | COL1A1
Description
collagen, type I, alpha 1 [Source:HGNC Symbol;Acc:2197]
Coordinates
chr17:48263678-48264067:-
Coord C1 exon
chr17:48264004-48264067
Coord A exon
chr17:48264001-48264003
Coord C2 exon
chr17:48263678-48263868
Length
3 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGG
5' ss Score
6.13
3' ss Seq
CTTGCCCTGCCCTACCACAGGAG
3' ss Score
7.96
Exon sequences
Seq C1 exon
GGCAGCCGCAAGAACCCCGCCCGCACCTGCCGTGACCTCAAGATGTGCCACTCTGACTGGAAGA
Seq A exon
GTG
Seq C2 exon
GAGAGTACTGGATTGACCCCAACCAAGGCTGCAACCTGGATGCCATCAAAGTCTTCTGCAACATGGAGACTGGTGAGACCTGCGTGTACCCCACTCAGCCCAGTGTGGCCCAGAAGAACTGGTACATCAGCAAGAACCCCAAGGACAAGAGGCATGTCTGGTTCGGCGAGAGCATGACCGATGGATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108821-66-82,67-82-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.853 A=NA C2=0.031
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(27.0=17.9),PF0141013=COLFI=PU(12.3=28.4)
A:
NA
C2:
PF0141013=COLFI=FE(28.8=100)
Main Skipping 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:
TGTGCCACTCTGACTGGAAGA
R:
GCAGGTCTCACCAGTCTCCAT
Band lengths:
104-107
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)