HsaINT1008055 @ hg38
Intron Retention
Gene
ENSG00000204248 | COL11A2
Description
collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187]
Coordinates
chr6:33178132-33178352:-
Coord C1 exon
chr6:33178308-33178352
Coord A exon
chr6:33178186-33178307
Coord C2 exon
chr6:33178132-33178185
Length
122 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
TCCCCTCACCGTGAATGCAGGGA
3' ss Score
5.35
Exon sequences
Seq C1 exon
GGAGATGACGGGGAGATTGGGCCTCGAGGGCTGCCTGGAGAGTCG
Seq A exon
GTGAGTGTCCAAGGGCTGGTGCTGGGGGAGGGGGCTCTGGGGAAGCCAGGAGGGGGACATGAGCACTAAAGGGACACAGTTTTATCCATTCATGCCGTCTCCTCCCCTCACCGTGAATGCAG
Seq C2 exon
GGACCTCGAGGTCTCCTTGGCCCCAAAGGCCCACCTGGTATTCCTGGACCCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204248:ENST00000374708:18
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(14.1=86.7),PF0139113=Collagen=FE(17.9=100),PF0139113=Collagen=PU(18.2=93.3)
A:
NA
C2:
PF0139113=Collagen=FE(21.8=100),PF0139113=Collagen=FE(22.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGATGACGGGGAGATTGGG
R:
GGGGGTCCAGGAATACCAGG
Band lengths:
98-220
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains