HsaINT0038476 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61944469-61945243:+
Coord C1 exon
chr20:61944469-61944601
Coord A exon
chr20:61944602-61945094
Coord C2 exon
chr20:61945095-61945243
Length
493 bp
Sequences
Splice sites
5' ss Seq
CCTGTAGGT
5' ss Score
3.22
3' ss Seq
CAACCCATGCTCTCGGCCAGCCA
3' ss Score
1.26
Exon sequences
Seq C1 exon
ATCTCTGTCCCAGGGAACCTCGGCACGGCCGTCCTGCCTGGCCTAGGGAGGCACACAGAGTACGACGTCACCATCTTGGCCTACTACAGGGACGGGGCCCGCAGTGACCCTGTGTCCCTCCGCTATACCCCCT
Seq A exon
GTAGGTGCCCCTCCACTTCCCCTCTGCTGGGTGTGGGGCAGGGATGGCCCAGGGGATCCCTGACTCACCCGCTGCACAGGCCCAGGACCCTAGACTCCCAGAACTGCTGGCTCCAGAGCCCTGATCACTGGGCCTGGTCGTTGGAGTCTGCAGCACTTCCTTGAGCTCACACGGGTATAGGTGTTCCCCCAGTGGCCGAGTGCACAAACCACCTAGTGTCCCGCAGGGCAGCCCAGGCAGCAGCCCTGGTTGGGGGTATGGTGAGGGCCCTGGCAGGTGGCGTGGTGTGGGTGTGGTGGGGTGCGGTGTGGGCAGTGGCAGGGGTGTGGTGTGGTTGTGCCAGGGGGGTGATGCGGGCTGTGGTAGGGGTGTGGCATGATGTGGTGGAGGCATTACGCAGAGCAGGGTAGGGGCTGGGCAGCTGGTCCTCTGGCCACCGGGTGCCTCCTTTCTGGAGGGGCCTGAGCCCCACACAACCCATGCTCTCGGCCAG
Seq C2 exon
CCACGGTGAGCAGGAGCCCACCCTCCAACCTGGCCCTGGCCTCGGAGACCCCCGACAGCCTGCAGGTCAGCTGGACGCCCCCGCTTGGCCGCGTGCTCCATTACTGGCTCACCTACGCCCCCGCCTCTGGCTTGGGACCCGAGAAATCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.200 A=NA C2=0.220
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(43.9=80.0)
A:
NA
C2:
PF0004116=fn3=PU(54.3=88.0)
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:
CCGTCCTGCCTGGCCTAG
R:
GGATTTCTCGGGTCCCAAGC
Band lengths:
254-747
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)