HsaINT0038186 @ hg38
Intron Retention
Gene
ENSG00000084636 | COL16A1
Description
collagen type XVI alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr1:31675007-31675311:-
Coord C1 exon
chr1:31675258-31675311
Coord A exon
chr1:31675040-31675257
Coord C2 exon
chr1:31675007-31675039
Length
218 bp
Sequences
Splice sites
5' ss Seq
CTGGTGGGT
5' ss Score
6.29
3' ss Seq
CACACATCTGTCTCTTGCAGGGA
3' ss Score
11.16
Exon sequences
Seq C1 exon
GGAGTGCCTGGAAACAACGGTTTGCCAGGACAGCCTGGGCTCACTGCAGAACTG
Seq A exon
GTGGGTACTGGCCAGGACTCCCTGTGCATGCCCCTTCCCTGCCCTTCCCAGGGCTGCTCAGGCTATGAAGCTGGCCCGGTAGCTGCAGTGGGGGTCCCTCTTCTCTCCCACTTCTGAGGCTGGAAGGTGCATGACGTGTCCCAAGGCTCTCCCTGATCCCATAAGTCTCCATGTTCCTTCCCCTCACCTGCTTGAGCCCACACATCTGTCTCTTGCAG
Seq C2 exon
GGATCCTTACCAATTGAACAGCACCTCCTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000084636:ENST00000373672:43
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=0.409
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(26.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(4.0=18.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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