HsaINT0037912 @ hg38
Intron Retention
Gene
ENSG00000060718 | COL11A1
Description
collagen type XI alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr1:102961866-102962265:-
Coord C1 exon
chr1:102962176-102962265
Coord A exon
chr1:102961920-102962175
Coord C2 exon
chr1:102961866-102961919
Length
256 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAA
5' ss Score
7.46
3' ss Seq
ATTTTTTTCACTTTTCCCAGGGT
3' ss Score
8.49
Exon sequences
Seq C1 exon
GGTGATCCAGGTCCTCAAGGTATCTCAGGGAAAGATGGACCAGCAGGATTACGTGGTTTCCCAGGGGAAAGAGGTCTTCCTGGAGCTCAG
Seq A exon
GTATAATCAATATCTATATAGATAAAGCAAGTGATTCCAATTGTTTATTAGAAGCATTTTTTCTCAGAACTTAAGAAGTGATGATTAAGGGAAGATATATAAACATATATATTTGATTATCATTACATATATGTGTATATATGTAGTTATGTCTATAAACATTACCTGACATCCTTATTTTACTAATCAGATATCTCCTCCTATTGGTATTCAATTCATATGGATTCATTTTCTTTATTTTTTTCACTTTTCCCAG
Seq C2 exon
GGTGCACCTGGACTGAAAGGAGGGGAAGGTCCCCAGGGCCCACCAGGTCCAGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000060718:ENST00000370096:40
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(15.2=40.0),PF0139113=Collagen=FE(39.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.3=100),PF0139113=Collagen=PU(19.8=94.4)
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