HsaINT0038824 @ hg38
Intron Retention
Gene
ENSG00000139219 | COL2A1
Description
collagen type II alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2200]
Coordinates
chr12:47986835-47987176:-
Coord C1 exon
chr12:47987078-47987176
Coord A exon
chr12:47986889-47987077
Coord C2 exon
chr12:47986835-47986888
Length
189 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGA
5' ss Score
10.65
3' ss Seq
GACCTGCCTCTCTTTTCAAGGGT
3' ss Score
9.39
Exon sequences
Seq C1 exon
GGTGCTCCTGGCATTGCTGGTGCTCCTGGCTTCCCTGGGCCACGGGGCCCTCCTGGCCCTCAAGGTGCAACTGGTCCTCTGGGCCCGAAAGGTCAGACG
Seq A exon
GTAAGAGCCCAAAGTGACCCCCAAGTTCCACTGACATCTCTGGAGTCAAACCCCATCACCCCTCTTTCCCATGCTCTCCTGCCCTGGCCTCACAGCGGCCTCCATCCGAGGGCATCTTGAACAGGGGTTCTGGGGAGGGGCAGGCTCCCTGGAGAGAATCTGGTGTGAGGACCTGCCTCTCTTTTCAAG
Seq C2 exon
GGTGAACCTGGTATTGCTGGCTTCAAAGGTGAACAAGGCCCCAAGGGAGAACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139219:ENST00000380518:21
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(16.1=42.4),PF0139113=Collagen=FE(38.1=100),PF0139113=Collagen=PU(37.5=81.8)
A:
NA
C2:
PF0139113=Collagen=FE(20.2=100),PF0139113=Collagen=FE(23.6=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:
CTCCTGGCATTGCTGGTGC
R:
TTCTCCCTTGGGGCCTTGTTC
Band lengths:
146-335
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