HsaINT1008052 @ hg38
Intron Retention
Gene
ENSG00000204248 | COL11A2
Description
collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187]
Coordinates
chr6:33178679-33178973:-
Coord C1 exon
chr6:33178920-33178973
Coord A exon
chr6:33178733-33178919
Coord C2 exon
chr6:33178679-33178732
Length
187 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACA
5' ss Score
8.92
3' ss Seq
GCTATCCTTCCTCCTCCTAGGGT
3' ss Score
9.31
Exon sequences
Seq C1 exon
GGCCGGGCAGGTGCTGATGGAGCCCGAGGGATGCCTGGAGATCCTGGAGTGAAG
Seq A exon
GTAACAGGCTTGGGCCCCTCCCTGAAGCCTGTAGCCTTCAGCCCACGCTGGGCTCAGTTGTTTCTTGGGGATGACCTAGTTCTCCAGGCTTCCCCAGGATCAGCACCCCCCCAGCTCAGGGTGCAGTAGGGAGGGGTGGGCTTGGACAGGGTCGTGTCCTCACTCTGGCTATCCTTCCTCCTCCTAG
Seq C2 exon
GGTGACCGAGGTTTTGATGGACTCCCAGGGCTCCCTGGAGAGAAGGGCCATAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204248:ENST00000374708:15
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(12.9=44.4),PF0139113=Collagen=FE(21.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.5=100),PF0139113=Collagen=PU(14.1=61.1)
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:
GGGCAGGTGCTGATGGAG
R:
CCTATGGCCCTTCTCTCCAGG
Band lengths:
104-291
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains