HsaINT0038819 @ hg38
Intron Retention
Gene
ENSG00000139219 | COL2A1
Description
collagen type II alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2200]
Coordinates
chr12:47989228-47989805:-
Coord C1 exon
chr12:47989761-47989805
Coord A exon
chr12:47989282-47989760
Coord C2 exon
chr12:47989228-47989281
Length
479 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
CATCCGCCTACTCTCTCCAGGGT
3' ss Score
8.63
Exon sequences
Seq C1 exon
GGTGCCCGAGGCAACGATGGTCAGCCAGGCCCCGCAGGGCCTCCG
Seq A exon
GTAAGTTCATTTCATCCTCAGCAGGTCATTGTTGCTGTGCTTTAAGTCCCGTTAAGCAGCCCAAGGCAGTCTGCAGGGTGTATTGGGTGCAACCACAGCAGCACTCTGATGTCTACTGGAAAGGGGGAGGAAAGAGAAGAAGTTTGTAAATATCAATTGAGCATATCGATAACAAGCTTTGAAGCATGGGCTCATTTTCCTCAGCCATCCTTTCAGCAGTCTTTTTAGAGGAGGGAGGTCAAAGGAGTTTCTGCTTCTCACCACAGATGTAGTCAGAAACTTGCTTTGCCTTCTGAAGCCAGGCAAAGTTTCCTGGGGACGCTGGCAATGGGGACAATTTTCATCCAAGGCCTTTTAGCCACAATGGATATGGAGTGAAATCAGTACAGAGGAGGGAAGGAGTGTGAGGTGTCGGGGTGGCTCGCTTTGGAGGCCAGAACTGGCATTCACCTCTCTTCTCATCCGCCTACTCTCTCCAG
Seq C2 exon
GGTCCTGTCGGTCCTGCTGGTGGTCCTGGCTTCCCTGGTGCTCCTGGAGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139219:ENST00000380518:17
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=FE(14.3=100),PF0139113=Collagen=PU(5.7=33.3)
A:
NA
C2:
PF0139113=Collagen=FE(17.3=100),PF0139113=Collagen=FE(19.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
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