HsaINT0038882 @ hg38
Intron Retention
Gene
ENSG00000168542 | COL3A1
Description
collagen type III alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2201]
Coordinates
chr2:188997165-188997389:+
Coord C1 exon
chr2:188997165-188997218
Coord A exon
chr2:188997219-188997335
Coord C2 exon
chr2:188997336-188997389
Length
117 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGT
5' ss Score
10.65
3' ss Seq
CTAACTGTTCTTGTTTTTAGGGT
3' ss Score
10.99
Exon sequences
Seq C1 exon
GGTGCTCCTGGTAAGAATGGAGAACGAGGTGGCCCTGGAGGACCTGGCCCTCAG
Seq A exon
GTACGTAGCTTTCCTCAATTTATTTCTAGCCTTCTAATAGATGCGTTCATCTCCAACCTTCTGACTTCTCTCTGTAATCTGTATTATTTCTACTTCCCTAACTGTTCTTGTTTTTAG
Seq C2 exon
GGTCCTCCTGGAAAGAATGGTGAAACTGGACCTCAGGGACCCCCAGGGCCTACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168542:ENST00000304636:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(8.2=27.8),PF0139113=Collagen=PU(23.4=83.3)
A:
NA
C2:
PF0139113=Collagen=FE(26.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGCTCCTGGTAAGAATGGA
R:
CTGGGGGTCCCTGAGGTC
Band lengths:
100-217
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