HsaINT1008048 @ hg38
Intron Retention
Gene
ENSG00000204248 | COL11A2
Description
collagen type XI alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2187]
Coordinates
chr6:33179431-33179805:-
Coord C1 exon
chr6:33179719-33179805
Coord A exon
chr6:33179488-33179718
Coord C2 exon
chr6:33179431-33179487
Length
231 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
CTGTCCCCCTGCTCCCCTAGCTG
3' ss Score
9.3
Exon sequences
Seq C1 exon
TTCCGGTTTGGCAGTGGTGGGGGTGACAAGGGCCCTGTGGTGGCGGCCCAGGAGGCTCAGGCCCAGGCGATCCTGCAGCAGGCGAGG
Seq A exon
GTGAGTGGGGCTGCTTCCCTGGAAAGGGAAGGCTCTGGGGGGCACTGGAAGGGTTGGCTGGAGTGAGTGTGCGGCAGGGGAGGCCTGGGTTGGTTTGGGGTTAACAGGGAGGTTGGGGAGAATCCTGGGCAGTGGATGAGGATCAGGAGAGGAAGGGTGAATTTGGAGAGTGCTGGGGCTGGGGGTTCCCACTGCCTGTCCCTCAGCTCTGCTGTCCCCCTGCTCCCCTAG
Seq C2 exon
CTGGCGCTCCGTGGACCCCCTGGCCCCATGGGATACACAGGGCGCCCTGGACCCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204248:ENST00000374708:11
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:
NO
A:
NA
C2:
PF0139113=Collagen=PU(25.8=84.2)
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:
TTCCGGTTTGGCAGTGGTG
R:
GCGCCCTGTGTATCCCATG
Band lengths:
132-363
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains