HsaINT0038470 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61941733-61942891:+
Coord C1 exon
chr20:61941733-61941862
Coord A exon
chr20:61941863-61942745
Coord C2 exon
chr20:61942746-61942891
Length
883 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
GTCCCTGCATGGCCCCCCAGCAC
3' ss Score
5.1
Exon sequences
Seq C1 exon
GTGGTGGTGGAGGGACCCGCCGCCTCCACGGAGCTGCACAACCTGGCCTCCCGCACAGAGTACCTGGTCTCCGTGTTCCCCATCTATGAGGGCGGGGTTGGCGAAGGCCTGCGGGGCCTGGTGACCACAG
Seq A exon
GTAGGTGGGGCAGAGGCAGCGGCCAGGTTCTGGGTGGGAGGCCCCACTCACGGCTGTCCCTTGGAGCCTGACACCCCAGGGCAGCATAGCGAGCAGCTCTGGATCTTAACCACCCACAGTTGGCACCATCCCCAGCTTGCTGTGTGACCAAGGCCGAGTCACTGGGCCCCTCTGACCCTGGGTGTTCTCTTCTGAACACCAGCTATACCGTTGGTGTCATCACCTCAACTGTAATCACAGCCCATTATGCTGCTTGTCCACAGTGTTCATGGAGCTCCCCCCTGCTTGGCCTCCAGCACGTGGCTTAGCTCGCTGGGTTCTTGGACCCCCAGGGACTGCCATGAGCCCGTCTGTAATAGCCTTGTTGAGATGTAATTTACACACCATACAACCTGCCCATTTAAAGTGTACAACTCCAGTGGCTTTGGTATATTCAGAGCTGTCACCCATGGCCACAGTTCATGTTAGATCATTTTCATCCCCCCAGAGGAACCCTGCACCCCTAAGCACCCGCCCCCCCAGCCACCCCAAGCCACCTTCTGTCTCTGGATGTGCCTGTCCCAGACGTTTCCTGCAGGTGGAATCACACAGTGCAGACTTTTGTGTCTGGGTGTTTCCCAAAGCCCTTTTCACCCCCCGGAGGCCACATTCCTCCCATGACCTCAAGGCAGATGGCCTTAGACAAAACTGTGGGGTGGCCTTGTGTCCCCAGAGCTGGAGCCACAAACCTTGGCCCAAGGTGAAGCCTGGGAAGTGCCACTTTGAATCCTGTGCACCTGCCAGGCGGTGGCCGTGCCCACCCACTCTGGTGTGAGGGTGCCCCGTGCGTGGGTGTGATCTCTGTGTGGGCTCCTTCCTAAAGTGTCCCTGCATGGCCCCCCAG
Seq C2 exon
CACCTCTGCCTCCGCCCCGGGCGCTGACCCTGGCCGCAGTGACGCCCAGAACCGTCCACCTCACCTGGCAGCCCTCGGCCGGGGCCACCCACTACCTGGTGCGATGTTCTCCTGCTTCCCCCAAGGGTGAAGAGGAGGAGCGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.341 A=NA C2=0.469
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(43.8=79.5)
A:
NA
C2:
PF0004116=fn3=PU(56.2=91.8)
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:
GTGGTGGTGGAGGGACCC
R:
CTCCTCCTCTTCACCCTTGGG
Band lengths:
270-1153
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)