HsaINT0037906 @ hg19
Intron Retention
Gene
ENSG00000060718 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:2186]
Coordinates
chr1:103444264-103444469:-
Coord C1 exon
chr1:103444416-103444469
Coord A exon
chr1:103444309-103444415
Coord C2 exon
chr1:103444264-103444308
Length
107 bp
Sequences
Splice sites
5' ss Seq
AAGGTATCA
5' ss Score
7.22
3' ss Seq
TTTTCTTTTCTTGGTGCCAGGGC
3' ss Score
8.54
Exon sequences
Seq C1 exon
GGTCCTCGAGGTTCAAGAGGTGCAAGAGGTCCCACTGGGAAACCTGGGCCAAAG
Seq A exon
GTATCACCTGTACTTTTTCTGTTTGGATGTTACTGTAGATTTTTTTTCCAGGCAGATGCTATGAGAAAGAATTCAAACTGATTTTTCTTTTCTTTTCTTGGTGCCAG
Seq C2 exon
GGCACTTCAGGTGGCGATGGCCCTCCTGGCCCTCCAGGTGAAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000060718-COL11A1:NM_001190709:33
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.866 A=NA C2=0.874
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(3.0=11.1)
A:
NA
C2:
PF0139113=Collagen=PU(12.5=53.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCCTCGAGGTTCAAGAGGT
R:
TCTTTCACCTGGAGGGCCA
Band lengths:
99-206
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)