HsaINT0038482 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61950410-61950948:+
Coord C1 exon
chr20:61950410-61950552
Coord A exon
chr20:61950553-61950838
Coord C2 exon
chr20:61950839-61950948
Length
286 bp
Sequences
Splice sites
5' ss Seq
ATGGTGACG
5' ss Score
2.49
3' ss Seq
CTCCACCCCTTCCCTGGCAGCCG
3' ss Score
7.68
Exon sequences
Seq C1 exon
TGACGTCTACCCAGCCCCCCTACCTCCAGAGCACACCATCGTCTTCCTTGTGCGCCTACTTCCCGAGACACCCCGTGAGGCCTTCGCGCTGTGGCAGATGACAGCCGAGGACTTCCAGCCCCTCCTTGGGGTTCTGCTGGATG
Seq A exon
GTGACGTGGGCCCCGCGTCGCCCCCAGCAGTCAGGAGGAGTAGGGGCAGGGAGGCCCCAGAGCCCTGGGAGGCCTTCAGAGGAAGTCCAGCCTCCAGGCCAGGCCCTCAGCACCCTCTGGGTGGGAGGCAGGTGTCCCGGGCAGGGGGCTGTGGGCCACATTGAGGGTCACCTCCAGCTTGGCACCCTCAGGGCTGCTCCTGTCCTGTCGTGGGGGCCGCCCTGCTCAAGGTATAGGCCCGGCTGGTTGCAGCCCGTTCTCACCTGCTCCACCCCTTCCCTGGCAG
Seq C2 exon
CCGGGAAGAAGTCCCTGACCTACTTCCACCGTGACCCCAGGGCTGCCTTGCAGGAGGCCACCTTCGACCCGCAGGAAGTGAGGAAGATTTTCTTCGGGAGCTTCCACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0221019=Laminin_G_2=FE(29.8=100)
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:
TGACGTCTACCCAGCCCC
R:
CTTGTGGAAGCTCCCGAAGAA
Band lengths:
253-539
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)