HsaALTD0001546-2/2 @ hg19
Alternative 5'ss
Gene
ENSG00000164692 | COL1A2
Description
collagen, type I, alpha 2 [Source:HGNC Symbol;Acc:2198]
Coordinates
chr7:94057065-94057789:+
Coord C1 exon
chr7:94057065-94057194
Coord A exon
chr7:94057195-94057197
Coord C2 exon
chr7:94057605-94057789
Length
3 bp
Sequences
Splice sites
5' ss Seq
GTGGTAGGT
5' ss Score
7.23
3' ss Seq
GAATGTTATTTTCTTAAAAGGTT
3' ss Score
6.46
Exon sequences
Seq C1 exon
GACTATGAAGTTGATGCTACTCTGAAGTCTCTCAACAACCAGATTGAGACCCTTCTTACTCCTGAAGGCTCTAGAAAGAACCCAGCTCGCACATGCCGTGACTTGAGACTCAGCCACCCAGAGTGGAGCA
Seq A exon
GTG
Seq C2 exon
GTTACTACTGGATTGACCCTAACCAAGGATGCACTATGGATGCTATCAAAGTATACTGTGATTTCTCTACTGGCGAAACCTGTATCCGGGCCCAACCTGAAAACATCCCAGCCAAGAACTGGTATAGGAGCTCCAAGGACAAGAAACACGTCTGGCTAGGAGAAACTATCAATGCTGGCAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000164692-76-81,77-81-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.885 A=NA C2=0.016
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(34.3=27.6),PF0141013=COLFI=PU(12.4=31.0)
A:
NA
C2:
PF0141013=COLFI=FE(28.1=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:
GAAAGAACCCAGCTCGCACAT
R:
GCATCCATAGTGCATCCTTGGT
Band lengths:
100-103
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)