HsaINT0037892 @ hg19
Intron Retention
Gene
ENSG00000060718 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:2186]
Coordinates
chr1:103468303-103468824:-
Coord C1 exon
chr1:103468771-103468824
Coord A exon
chr1:103468348-103468770
Coord C2 exon
chr1:103468303-103468347
Length
423 bp
Sequences
Splice sites
5' ss Seq
CCTGTATGT
5' ss Score
4.27
3' ss Seq
ATACTTTTTCTTCATTGCAGGGT
3' ss Score
9.93
Exon sequences
Seq C1 exon
GGCCCACGAGGTTTGCTGGGTCCAAGGGGAACTCCAGGAGCTCCAGGGCAGCCT
Seq A exon
GTATGTATTGCTGGAAACATTGAAGATTTTCTAGGGAAAGCTTGTTGCCAACCTTTTAGAGGCCATAAAAGCCCTCAGTAGAGAGCCAAGAGTTTATTGCCTTGTTATGTTTGAAGATCTATTGTTGCTGCCTTTCACTTTAACTCATCATTCCCTCCTTTTCTTCTATCTTCCTTTTGATTATCTATCTTAGTGTTTTCATGATACATCCCCAGCATGCAGAGGAAAATGTTGCTAGATTGTCTCCAATGTGGACATGGAAAAGAAAGTATAGGTCTTGTCTCTTCTTCGTTTCCATTAAATCCTAAAATGATTTTTAGTTGCTTAGGGTAGTGAATATCATGATATTAGATTAGTCTTTTTGATTTTCTGTTTTAGCATCAAAACATATAAACAACCATAAATACTTTTTCTTCATTGCAG
Seq C2 exon
GGTATGGCAGGTGTAGATGGCCCCCCAGGACCAAAAGGGAACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000060718-COL11A1:NM_001190709:20
Average complexity
IR-S
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(23.6=100),PF0139113=Collagen=FE(26.6=100)
A:
NA
C2:
PF0139113=Collagen=FE(16.1=100),PF0139113=Collagen=PU(14.3=80.0)
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:
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
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)