HsaINT0038215 @ hg38
Intron Retention
Gene
ENSG00000084636 | COL16A1
Description
collagen type XVI alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr1:31696963-31697300:-
Coord C1 exon
chr1:31697220-31697300
Coord A exon
chr1:31697089-31697219
Coord C2 exon
chr1:31696963-31697088
Length
131 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
CCCGCTCTTCCACCAAACAGTGC
3' ss Score
7.12
Exon sequences
Seq C1 exon
TTTGACCTTCAGCAGGTGCACATCTACTGTGACCCGGAGCTCGTGCTGGAGGAGGGCTGCTGTGAGATTTTACCAGCAGGG
Seq A exon
GTGAGTGGCCCGGCCCTTGGGCTGCCCAGGGACACACTGTGCTGGAGATGAGGGTCTGGAAGGTGATGCCTGGAGGTCTTAGGAGGAGTCTGCTCCTGTACTGACCCTAGCCCCGCTCTTCCACCAAACAG
Seq C2 exon
TGCCCCCCAGAGACCTCCAAGGCCCGCCGGGACACCCAGAGCAATGAGCTCATTGAGATCAATCCACAGTCTGAAGGCAAGGTCTACACCCGCTGCTTCTGCCTGGAGGAGCCTCAAAACAGCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000084636:ENST00000373672:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.420
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CCTTCAGCAGGTGCACATCTA
R:
CTCGCTGTTTTGAGGCTCCTC
Band lengths:
202-333
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