HsaALTD1023061-2/2 @ hg38
Alternative 5'ss
Gene
ENSG00000139219 | COL2A1
Description
collagen type II alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2200]
Coordinates
chr12:47997606-47997924:-
Coord C1 exon
chr12:47997879-47997924
Coord A exon
chr12:47997871-47997878
Coord C2 exon
chr12:47997606-47997707
Length
8 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
CTTTTTCTCTTTATGCCAAGGGT
3' ss Score
5.52
Exon sequences
Seq C1 exon
GGACCTGCAGGGGAACAAGGACCCAGAGGGGATCGTGGTGACAAAG
Seq A exon
GTGAAAAA
Seq C2 exon
GGTGCCCCTGGACCTCGTGGCAGAGATGGAGAACCTGGGACCCCTGGAAATCCTGGCCCCCCTGGTCCTCCCGGCCCCCCTGGTCCCCCTGGTCTTGGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139219-11-11,12-11-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(30.9=100),PF0139113=Collagen=FE(25.4=100)
A:
NA
C2:
PF0139113=Collagen=PD(5.5=8.8),PF0139113=Collagen=FE(49.3=100)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGGGAACAAGGACCCAGAG
R:
AGGATTTCCAGGGGTCCCAG
Band lengths:
93-101
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains