HsaINT0038496 @ hg19
Intron Retention
Gene
ENSG00000101203 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:14670]
Coordinates
chr20:61960937-61962285:+
Coord C1 exon
chr20:61960937-61961013
Coord A exon
chr20:61961014-61962071
Coord C2 exon
chr20:61962072-61962285
Length
1058 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CCTCCCTTCTCTCCTGCCAGGAC
3' ss Score
12.17
Exon sequences
Seq C1 exon
GGGAGCCTGGAGCTGTTGGTCAGATGGGCAGCCCTGGGCAGCAGGGGGCTAGCACCCAGGGCCTCTGGGAGTGACAG
Seq A exon
GTGAGCCCCTGCTGCCTGCATCTATCTGCCAAGGCTGAGGGCATCCAGGAAGGAGGAGCTCCTGAGGGGCCAACGGGTGGGGCCTCATGCTGTCCAGGGTGGGGTGCTGGGAGCACAAGGCCCAGCAGAGGCAGGCGAGGTGGCCCTGGGGAAAGTAGGGTCAACTATGGACCCCGTAGGGGCAACAGGAATGTGGGGTCACAGGGTGTGGGGTCACAGGGCGTGGGGTCACAGGACGTGGGGTTCCGGAGATGGATTGGCGTGCTGGGAGTCTGCTGCACCTCGTGGGATGCAGAGTTGCGTGCTGGGGCGGAGGAGGCCCTGACCAGGGTTAGCGCAGCAGGGAGAGTGGAGCTCAGGTGTTTGCTCAGTGGGCACCTGGTCCAAGTGTGGGAAAGCTCACAGGAGTCCCAGGAGGGGCCTGTGAGGCCCTGGGTATGTCGATGAGAGAGGCAGGGTGGGGGCCATAGTAGCACCAGGTAACCTCTGCCTTCCTCAGGAAGCGCTGGGCAGGCGGACCCTGTGTGCAAACTTAGCTGAGGGGCTGGTCCCAGCAGCAGGTGTGGGGACAGGGTCCCAGGAGCAGGTGGTGGGTACAGCACAACTCCGGCCTCAAGTAGCTTCAGGGGCCAGAGCGTGGCGCAGGGTGTGTGACCTGGGGCCCATGAGGGGCCGGCACCTTTGAGCTAGGGGACTCGGCAGGGGCTAGGAGGGCTGAGGAGCACAGGCAGGAGACCCAGGGGCTCCTGGTAAGGCTGGGGCAAGAGGGCAGCTGCCTGAGATGCCCAAGAATCAGGTCAGAGCCCAGGGCTAAGAACAAGCAGCCTTGCTTCTCCTCCACAGACCCGTCAGAGAATGACCCCACCCACGGCCCTGCCCGCAATCCTGCCCACTTACGGCCCTGCCCATGGCTCTGCCCACTCACGGCCCTGCTGGACGCAGTGTGCAGAGACCCAGGATGCGGGCTCTCAGGGTGGCCACAGTGCCAGGCGCTGGCCCTGAGCCGGTGTCCAGCTGTCTTCGGCCTCTCACATCTGTCCTCCCTTCTCTCCTGCCAG
Seq C2 exon
GACATTTTCTGCACTGCCCCGAGGAACGCTGAGCCTTCCTCCCTGGGTTTGTCTGGACACCGAGAGCGACCACATCCTGGAGAAGCCAGGAGAAAAGCTCAGGAAGAGCCTGCAGGTGGAAGGAGAGGGAAGCAGCGGCCTCGGCCAAGGCCCACCCCATACTCTTGGCTCTGTAGCATTTCCAAGTTCAGATAAACCCCTGAGTGCTCACCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101203-COL20A1:NM_020882:35
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTGGAGCTGTTGGTCAGAT
R:
GGGTGAGCACTCAGGGGTTTA
Band lengths:
286-1344
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)