HsaINT0038500 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61939323-61940058:+
Coord C1 exon
chr20:61939323-61939442
Coord A exon
chr20:61939443-61939893
Coord C2 exon
chr20:61939894-61940058
Length
451 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGG
5' ss Score
10.88
3' ss Seq
TTATTCCTGCTGCTCCCAAGGCC
3' ss Score
5.54
Exon sequences
Seq C1 exon
GCCTGACTCAGTACAGCGGGGATGCTCAGACTGAGTGGGACCTGAACTCCCTCAGCACCAAGGAACAGGTGCTGGCAGCTGTGCGCCGCCTCCGCTACAAGGGGGGGAACACGTTCACAG
Seq A exon
GTACGGCCCAGGCCTGCCCCTCCCTCTGTCCTGAGGGCGGACCTCCTTCTGCCGCCCTCCCAGATCCCGAAAGCTTGTGTGTAAATCGAGCTCCAAGTGGTGTGGACCTGAGCCCTGTTCACACCTTTATAGAGGGCAGAGTCACCCCCTTGTTTACCTTTGATGAAAACGAGGGCCTGTGTCCAGCGCGTGGCTCCTCTGTTCCACATTAGCAGCTCTGGCTGGGTCCACACCCGGCCCAGTCTGGGTGCTCACCTTGCAGGTAGGGTCTGGCTGGGGAACTTGGGGCCCTTCAACAGGTAGACCCTCCCTGCTCCCTTGGGCTGCTGCGGGGCCTCCTGATACCCCACAAGGGAAGGAGAGGAGCATCTCTGCTGTCCGGTTGCTGCCAGCCGAGCACCAGGAGGGGATGCTGGCAGCTGCCTGTCACTTTATTCCTGCTGCTCCCAAG
Seq C2 exon
GCCTTGCCCTGACCCACGTGCTGGGGCAGAACCTGCAGCCGGCGGCTGGCCTCCGTCCAGAGGCAGCCAAGGTGGTGATTCTGGTGACGGACGGCAAGTCCCAGGACGATGTGCACACTGCTGCCCGTGTCCTCAAGGACCTGGGCGTGAACGTCTTCGCTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.077 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(23.7=100)
A:
NA
C2:
PF0009223=VWA=FE(32.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGACTCAGTACAGCGGGGAT
R:
CCACAGCGAAGACGTTCACG
Band lengths:
283-734
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)