RnoALTD0007313-2/2 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000003897 | Col1a1
Description
collagen type I alpha 1 chain [Source:RGD Symbol;Acc:61817]
Coordinates
chr10:82748047-82749148:+
Coord C1 exon
chr10:82748047-82748148
Coord A exon
chr10:82748149-82748480
Coord C2 exon
chr10:82749080-82749148
Length
332 bp
Sequences
Splice sites
5' ss Seq
TCGGTCCCC
5' ss Score
-7.3
3' ss Seq
TTTTTCTCTTGTTTTTCTAGAAC
3' ss Score
11.72
Exon sequences
Seq C1 exon
GGACCTGTTGGCCCCCCTGGACAAGATGGCATCCCTGGACAGCCTGGACTTCCTGGTCCTCCTGGTCCCCCCGGCCCCCCCGGACCCCCTGGTCTTGGAGGA
Seq A exon
GTAAGTAGATCTGGGAGACCCCAGACTTATGTGACTCCCCGTTTTGTTTTGTTTTTGTTCATTTGCCTGTTTGTTTTTCTTTGCTTTGGTTTTGTCAGACACAACTTTGTATCTTTAAGTAATCATAAACTTACAGGAAAGTTGCAATGGTACACAGAACTTCTGTTCACCCTTCAAAACACCTGCTTTTTCACTTTCTGGACACACAGCTCTCTCTGTCTCTGTGTATTCCCAACCATTTGAGACATATCGTCAAGAACATGCCCAAAGGGGGTTGGGGATTTGGCTCAGTGGTAGAGCGCTTGCCTAGCAAGCGCAAGGCCCTGGGTTCG
Seq C2 exon
AACTTTGCTTCCCAGATGTCCTATGGCTATGATGAGAAATCAGCTGGAGTTTCCGTGCCTGGCCCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003897-8-8,9-8-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(57.9=100)
A:
NA
C2:
PF0139113=Collagen=PD(10.5=26.1),PF0139113=Collagen=PU(6.5=17.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]