HsaINT0038217 @ hg19
Intron Retention
Gene
ENSG00000084636 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:2193]
Coordinates
chr1:32161689-32162689:-
Coord C1 exon
chr1:32162564-32162689
Coord A exon
chr1:32161743-32162563
Coord C2 exon
chr1:32161689-32161742
Length
821 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGT
5' ss Score
7.07
3' ss Seq
TCTTTGCTCTGTCTGCCCAGGTG
3' ss Score
9.67
Exon sequences
Seq C1 exon
TGCCCCCCAGAGACCTCCAAGGCCCGCCGGGACACCCAGAGCAATGAGCTCATTGAGATCAATCCACAGTCTGAAGGCAAGGTCTACACCCGCTGCTTCTGCCTGGAGGAGCCTCAAAACAGCGAG
Seq A exon
GTGGGTGGGCAGGACAGGTGGATGCCAGCACAGGCAGGCACAAGTGAGATACCCCTCCCCTGAGCTGACTGACGTCTGCCACCAGGGTCAGTTGGCCATGGGCCCAGGGCAGGAGGGGCACTGGAAGCCCTCCCTATTTGTACGCCACCCCTAAATGATTCAGGGAGGCAGAGACAGCCCACTGGCCACCACTGGGTGGCCCTGTGCCCACCTACCTATGGGTGTTGAGAGTGGTACCATCTAGCTCTGGCACTGCCTAGACCCTCACGGATGCCATCCAGACTCTTCTGATGAGGGCAGGACCAGGCTTGTCCCTCAAAGCCAGTTTCTCCAGAACAGAGATACCTGGGATCAGAGGTCAGGTCATACTGCTTCCCCCCAGGGATGGCTCACTCTCCTGGGCCCAGCGCCGGCCAGGGCCAGACTGGTTTTACACCCAGCACCATGGCCAGCTGTCTGCCCACTCTCAGGTTCTTTAGAGGTGGCATGGAAGCCTGGTTCCTCCTTTAGCCCCACCCCCTGGCTGGGCACTCTCCCTGCCCGCTCGGGCATCTTGCCCAGCCTTGGGCTGCAGGAACACAGGATCCCATTGATGCATGGTCTTGTTGGCTCTGACATCACATGGGTGGGTGGGGGGGGAAGGAGGGGGACCTGTTGGGGCAGCCACAGGGGCCTGAGCAGGCCCTTGATGCCCCAGGAGGTGCCAGATGCCAGGCTGAAGGATTACCTGGGGCCCATGCCCCCTGCCTGGGTGCCCCTTTCCAGCCTGGACCCCAGAACTTCCCCCTCCTCAAGGGTTTCTCTTTGCTCTGTCTGCCCAG
Seq C2 exon
GTGGATGCCCAGCTGACGGGAAGAATCAGCCAGAAGGCAGAAAGGGGAGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000084636-COL16A1:NM_001856:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.421 A=NA C2=0.951
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(12.5=38.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)