HsaINT0037904 @ hg38
Intron Retention
Gene
ENSG00000060718 | COL11A1
Description
collagen type XI alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr1:102979060-102979435:-
Coord C1 exon
chr1:102979382-102979435
Coord A exon
chr1:102979105-102979381
Coord C2 exon
chr1:102979060-102979104
Length
277 bp
Sequences
Splice sites
5' ss Seq
CGGGTATGA
5' ss Score
7.63
3' ss Seq
AATTGAACTGTCTTTGCTAGGGA
3' ss Score
5.57
Exon sequences
Seq C1 exon
GGTTCCACTGGATTCCCTGGGTTTCCAGGTGCCAATGGAGAGAAAGGTGCACGG
Seq A exon
GTATGATATATAAATATGTTTTGAACTATGTATATAAGTGTTCTTAGCTGGACATAGTGGTGTGTGCCTGTATTCCCAGATATTTGTGAGGCTCAGGTGGAGGATTGCTTGAATCCCGGAGTTCCAGGCCAGCCTGGGCAGCATAGCAAGTCTGTCTCTAAATGAATACGAATGAATGAATGAATGAATGATGTTCTTGCATGACTACTCAGTCTCAGCACCAGGCTCATAATTTACTGTGATATACTGCATATTGAAATTGAACTGTCTTTGCTAG
Seq C2 exon
GGAGTAGCTGGCAAACCAGGCCCTCGGGGTCAGCGTGGTCCAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000060718:ENST00000370096:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.900 A=NA C2=0.987
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(3.9=16.7),PF0139113=Collagen=FE(23.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.9=100),PF0139113=Collagen=PU(8.5=33.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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