HsaINT0037889 @ hg19
Intron Retention
Gene
ENSG00000060718 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:2186]
Coordinates
chr1:103470000-103470217:-
Coord C1 exon
chr1:103470164-103470217
Coord A exon
chr1:103470045-103470163
Coord C2 exon
chr1:103470000-103470044
Length
119 bp
Sequences
Splice sites
5' ss Seq
AGGGTATGT
5' ss Score
8.34
3' ss Seq
ATTCATTTTGTCAATGACAGGGA
3' ss Score
6.11
Exon sequences
Seq C1 exon
GGTGAACGAGGTCCTCAAGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGG
Seq A exon
GTATGTTAATACTTCTTTTCTTAAGAAATATTTAAAATTAAAACATAATAAAACAAAATCATGTTGAAATGATACATTGTCCAAATGTTCTATACTCTCATTCATTTTGTCAATGACAG
Seq C2 exon
GGAGAAGATGGAGAAATTGGACCAAGAGGTCTTCCAGGTGAAGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000060718-COL11A1:NM_001190709:18
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(25.0=100),PF0139113=Collagen=PU(20.0=94.4)
A:
NA
C2:
PF0139113=Collagen=PD(15.4=66.7),PF0139113=Collagen=FE(19.4=100),PF0139113=Collagen=PU(17.2=73.3)
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:
TGAACGAGGTCCTCAAGGTCC
R:
TTCACCTGGAAGACCTCTTGG
Band lengths:
94-213
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)