MmuALTD1000628-1/2 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000001506 | Col1a1
Description
collagen, type I, alpha 1 [Source:MGI Symbol;Acc:MGI:88467]
Coordinates
chr11:94950338-94950899:+
Coord C1 exon
chr11:94950338-94950570
Coord A exon
NA
Coord C2 exon
chr11:94950709-94950899
Length
0 bp
Sequences
Splice sites
5' ss Seq
AGAGCGGTA
5' ss Score
-23.58
3' ss Seq
CTTTGCCTTGCCCACTTCAGGAG
3' ss Score
8.55
Exon sequences
Seq C1 exon
TGGCGGTTATGACTTCAGCTTCCTGCCTCAGCCACCTCAAGAGAAGTCTCAAGATGGTGGCCGCTACTACCGGGCCGATGATGCTAACGTGGTTCGTGACCGTGACCTTGAGGTGGACACCACCCTCAAGAGCCTGAGTCAGCAGATTGAGAACATCCGCAGCCCCGAAGGCAGCCGCAAGAACCCTGCCCGCACATGCCGCGACCTCAAGATGTGCCACTCTGACTGGAAGA
Seq A exon
NA
Seq C2 exon
GAGAGTACTGGATCGACCCTAACCAAGGCTGCAACCTGGACGCCATCAAGGTCTACTGCAACATGGAGACAGGTCAGACCTGTGTGTTCCCTACTCAGCCGTCTGTGCCTCAGAAGAACTGGTACATCAGCCCGAACCCCAAGGAAAAGAAGCACGTCTGGTTTGGAGAGAGCATGACCGATGGATTCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001506-70-59,71-59-1/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.863 A=NA C2=0.125
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 Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGACCTCAAGATGTGCCACTC
R:
TTGCAGTAGACCTTGATGGCG
Band lengths:
93-96
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types