HsaINT0038823 @ hg38
Intron Retention
Gene
ENSG00000139219 | COL2A1
Description
collagen type II alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2200]
Coordinates
chr12:47987078-47987313:-
Coord C1 exon
chr12:47987269-47987313
Coord A exon
chr12:47987177-47987268
Coord C2 exon
chr12:47987078-47987176
Length
92 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
CCTTCTTCTCATGCCCACAGGGT
3' ss Score
11.66
Exon sequences
Seq C1 exon
GGTAACCCTGGAACAGATGGAATTCCTGGAGCCAAAGGATCTGCT
Seq A exon
GTGAGTGTTGCCCGTGGACTTTGCTACCCCAGGAGAGCCCAGTCCTGCCTCTCCCCTCTCCTGACACCCCTCCCTTCTTCTCATGCCCACAG
Seq C2 exon
GGTGCTCCTGGCATTGCTGGTGCTCCTGGCTTCCCTGGGCCACGGGGCCCTCCTGGCCCTCAAGGTGCAACTGGTCCTCTGGGCCCGAAAGGTCAGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139219:ENST00000380518:20
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(16.1=100),PF0139113=Collagen=FE(16.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(16.1=42.4),PF0139113=Collagen=FE(38.1=100),PF0139113=Collagen=PU(37.5=81.8)
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:
TGGAACAGATGGAATTCCTGGA
R:
GTCTGACCTTTCGGGCCCAG
Band lengths:
135-227
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