HsaINT1008102 @ hg38
Intron Retention
Gene
ENSG00000204248 | COL11A2
Description
collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187]
Coordinates
chr6:33165549-33165984:-
Coord C1 exon
chr6:33165931-33165984
Coord A exon
chr6:33165817-33165930
Coord C2 exon
chr6:33165549-33165816
Length
114 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
CCATCTGTCCCTGCACCCAGGGT
3' ss Score
8.95
Exon sequences
Seq C1 exon
GGCCCAGGCGGACCCAAGGGAGAGAAGGGTGTGCAGGGCCCTCCAGGACACCCG
Seq A exon
GTGAGTGAGGAGTCAGGGCTGCTCCCAGGGCCGTACCCCTCTGCTCCACTGCTGCCACACTTCACCCTCACACCAACCTTGTCTCTTGCCCTCTCCATCTGTCCCTGCACCCAG
Seq C2 exon
GGTCCCCCAGGCGAGGTGATCCAGCCACTGCCCATTCAGATGCCCAAGAAGACTCGGCGCTCGGTGGATGGAAGCCGTCTGATGCAGGAAGATGAGGCCATACCGACCGGGGGAGCCCCCGGCAGTCCTGGGGGGCTGGAGGAGATCTTTGGCTCACTCGACTCCCTGCGGGAGGAGATCGAGCAGATGAGGCGGCCAACAGGGACCCAGGACAGCCCTGCTCGCACCTGCCAGGACCTGAAGCTGTGCCACCCAGAGCTTCCCGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204248:ENST00000374708:60
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.933
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(12.7=8.9),PF0141013=COLFI=PU(41.5=30.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGGGAGAGAAGGGTGTGCAG
R:
CTGTCCTGGGTCCCTGTTGG
Band lengths:
254-368
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains