HsaINT0038831 @ hg38
Intron Retention
Gene
ENSG00000139219 | COL2A1
Description
collagen type II alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2200]
Coordinates
chr12:47984087-47984599:-
Coord C1 exon
chr12:47984546-47984599
Coord A exon
chr12:47984141-47984545
Coord C2 exon
chr12:47984087-47984140
Length
405 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
TCTTTTTCTCTTCTGTCTAGGGT
3' ss Score
10.6
Exon sequences
Seq C1 exon
GGTGAGCCTGGCAAAGCTGGTGAGAAGGGACTGCCTGGTGCTCCTGGTCTGAGG
Seq A exon
GTAAGTATCCTTCCCCGCTGCCCATGACTTGGTGTTGGCCGGGCATCTGCAGGGAGGACAGGGGAACGGCCTCCCCATGGCATGGTCCCGGGACCCCTCAGTATTGAGTGTTGATCTCTGTGGCTGAGCCCCATGCTGGCTGGGCCCTTTGGGTGTCTACACAGGGAGACTTCTGTTTGCCATTGGTCAGCAGGCCGGGGAGCTGGGGAAGGCTTCCATGCTGAGAACAGCTAAGAAAAGACGGGGCCTGGGAAGGAAGGGAGGGGAAGGTGTGGAAATGGAGCTCAGCTGGGGTACCGTGGAGGTCTGGAAACTCTGGGCCAGAAGTACCTTTGCCCAATCCTAGGGGGACTGCAAGTGGGAAGAAAAGCGTGTCATTGACTTTTCTTTTTCTCTTCTGTCTAG
Seq C2 exon
GGTCTTCCTGGCAAAGATGGTGAGACAGGTGCTGCAGGACCCCCTGGCCCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139219:ENST00000380518:28
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:
NO
A:
NA
C2:
NO
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:
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]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development