HsaINT0038211 @ hg19
Intron Retention
Gene
ENSG00000084636 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:2193]
Coordinates
chr1:32120915-32122045:-
Coord C1 exon
chr1:32122001-32122045
Coord A exon
chr1:32121104-32122000
Coord C2 exon
chr1:32120915-32121103
Length
897 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
CTAAGTATCTATCTTTGTAGGGT
3' ss Score
6.47
Exon sequences
Seq C1 exon
GGACCCCCTGGAAAGCAGGGATTCTATGGACCTCCTGGTCCCAAG
Seq A exon
GTGAGTGGGCACTGGCTGGGCTTGAGAGGAGAAGCTCACGAGTGGATGAAGCCCAGCTGCAAGTTACGGCTTTAGCCACAGAGAGGAGACACAGGAAGGCCAGTGGGCAGGGGGCAAAAATGCAGAACTTGGAGCAGGATAGTGTCTGAAAATTTCTCACATGGGGTCATTAGCTGTGGTTGGGGGGAAGGAAATCTCCAGTTCATTTACTCACTGATTGACTGATTGATTCATTCATTGTTTCCATTTCCCGAGCACTCCCTTGCTCCTGCTCACATTCCAGGCCCTTGTCCTGGCCTCAGGTAAACAGAGGTCCCTGAACAATAGGTGCTCACAATAGACCAGTCACACTTACACTAGGGATTGGCAAGTTTTCCAGAAGACATGAGACATAGCGCTGTGGGATGAGAGGGAGGAGCACCCAACCCAGCCTGGGGAGTCGGAGAGGCTGCAGAGAGAACAGGAACACTTCAGCTCAGGAGGGGTGCACTGGATAGAGAGAGATGAGGGGAAGGGCATTCAGGACCATAACAACATGGCAGAATCAGAGAATCATCACCAGTGAGGTCTGGTGGGAGGCAGAGGGTGGGGAGAGGAGGCTGAGGAAGGAACGATCAGGACCACATAATGAATGGCCTTGCATGCCCGGCCAACGAATGAGTGCTTTATCCTGAGGACATTTGGGAGCCATCAGAATTTCTAAGCAGGGAGTAACACCAGGAGAACTGTCTTCTAGAAGGACCACTCTGGGGCAGTGAGGTGGAGTGACCTGTCAGGATGCTGTGGCCACAGTCTAGAGGGAGACGCTGGGGGCCTGGTGGGAGGGTGGAGAGAAAAGAGCAGATTGGTGAGACATCATGATGTAAATTTGACAGCACTAAGTATCTATCTTTGTAG
Seq C2 exon
GGTGATCCAGGAGCTGCAGGACAGAAGGGCCAGGCAGGAGAGAAGGGGAGAGCCGGCATGCCTGGTGGACCTGGCAAGAGTGGTTCCATGGGGCCTGTTGGGCCACCGGGCCCTGCAGGAGAGAGAGGCCACCCTGGAGCTCCGGGGCCTTCGGGGAGCCCTGGCTTGCCTGGTGTGCCTGGCTCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000084636-COL16A1:NM_001856:66
Average complexity
IR-S
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=FE(23.3=100)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCTGGAAAGCAGGGATTCT
R:
CATGGAGCCAGGCACACC
Band lengths:
230-1127
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)