HsaINT0038475 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61944144-61944601:+
Coord C1 exon
chr20:61944144-61944286
Coord A exon
chr20:61944287-61944468
Coord C2 exon
chr20:61944469-61944601
Length
182 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGC
5' ss Score
6.32
3' ss Seq
TGGGGCTCTCCTCTCCCTAGATC
3' ss Score
10.6
Exon sequences
Seq C1 exon
AGAAAGCTCCCAGCCCAAGCCAGCTGTCCATGACGGAGCTGCCAGGGGATGCAGTCCAGCTGGCGTGGGTGGCCGCAGCCCCGTCTGGCGTGCTTGTCTACCAGATCACGTGGACGCCCCTGGGAGAGGGGAAGGCTCACGAG
Seq A exon
GTGGGCAGGGGTGGGTTTGTCCTTCCGAGGGGCCCCCCGTGGGCCCCTAGTCCTGAAGCCAAAGTCTAGGGCTCAGAGCCATATGTGCGCCCACCCTGTCTCCCAGGGATGCCTCACTGCCCGGCCCCCCAACCTGAGGACCCCACTGCACCCGGTGACCCCTGGGGCTCTCCTCTCCCTAG
Seq C2 exon
ATCTCTGTCCCAGGGAACCTCGGCACGGCCGTCCTGCCTGGCCTAGGGAGGCACACAGAGTACGACGTCACCATCTTGGCCTACTACAGGGACGGGGCCCGCAGTGACCCTGTGTCCCTCCGCTATACCCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.271 A=NA C2=0.200
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.7=91.7)
A:
NA
C2:
PF0004116=fn3=PD(43.9=80.0)
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:
CCAAGCCAGCTGTCCATGAC
R:
GTATAGCGGAGGGACACAGGG
Band lengths:
257-439
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)