HsaINT0039825 @ hg19
Intron Retention
Gene
ENSG00000092758 | COL9A3
Description
collagen, type IX, alpha 3 [Source:HGNC Symbol;Acc:2219]
Coordinates
chr20:61461869-61463541:+
Coord C1 exon
chr20:61461869-61461940
Coord A exon
chr20:61461941-61463505
Coord C2 exon
chr20:61463506-61463541
Length
1565 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGT
5' ss Score
10.75
3' ss Seq
AGCCTTCTCTCCACATCCAGGGT
3' ss Score
7.61
Exon sequences
Seq C1 exon
GGCCAGAAGGGCAGCATGGGAGACCCCGGCCTTCCAGGCCCCCAGGGCCTCCGAGGTGACGTGGGCGACCGG
Seq A exon
GTAAGTGGCCCTCTCAGCAGGAAGCTCCCCTGCACCCCCTCTACCCATGTACCACAGTCCCCCACCCCCATGACAGTCCCCCAACCCCCACCACAGTCCCCCAACCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCACCCCCTACCACAGTCCCCCAACCCCCACCACAGTCCCCCACCCCCTACCACAATCCCCCACCCCCCACCACAGTCCCCTGGGACGCAGACAGGGAGAGGCCCTTGCAGCTCCCAGTGGGAAATCTGGCCATGGGCAGTGTCTCCCTGCGTGGCGGAGGCAGTGGCATCAGGGCCCCGACTGTGGCGCCTTTGGCCCCTCTGACCTTCCACGTGGTGTTCCTTGTGGGTGGGAGGCTGCGGGAGCCTGGGCCGCTCTGCCTCCTGCCCTGCGTAGACGCCTGGCGGGACCTGCACACGGTCAGTGTTCATTCCTCGAGATTGGCGTGGAGGCTGAGGCTCAAGAGCCACGCCTGCTCCCGCCTAGCGGGTGTCTGCGGAGGCGCGGTTGACAGAGGATCACGTTGCTATAAAATAGGTTTGAACACCATGTCCCAAGTGACTGTAACGGTCACAGCTTCTACCTCGTCAAGACTTTTTCCTGCTGGTCTTGCAGCAGCTGCAGCATTAGCTCCTTGGGGGTCCGGGCAGAAGCGGGGCACGGCCTACCCAGGGCCCCAGCTCACTGGAAGGAGCCTGTGGGTCTGGTCTGGGCCCCAGCCATGCTCCACCAGGTCCTTGGGGACCTCGTGTGCCTGCTGTGGCCACCTCTGCTGGGCAGACAGACCCCTTTTTAGATGTCAATCCCGAGAAGCCTCCAGGACACGGCTGCAGATGCCCCGTCATTCCAGGGTGATGGTCATTCCAGGGTGATGGCCGGGGCTGTGGACACCACCACCCCATGGGGGATAGCGGGCTGTTTATTGGCCTCCAGGCAGGACATTCCAGAGGTGGGGGCCATGCCAGCAACCTCAGGGCCTCCGAGAGATGGCAGGGCTGGCACCCGCCCTGCGGGCACTGCGCCTGTCCCAGGTGTGGGTGGGGCCTGGTGGCTGAATTTCCCTTTCACTTTAAACTCACGGGAAAGTCTCCTGCTTTTCTGCCCTTTGGGCCAGTTCTCACTTATGTGGCCATGTGAGCAAATGGACATTTTTTAAAGGGATTCATAGCAACTCCCAGACATGTCCTCATTTCACAATGCCGGGGGAAGGTGATTAGATGAGCTTTTGCATCTTTGACTCTACTGTGACGGAATTATCCTGCAATTGTGCAGAAACACCCGCACGAATTCACGGGTGTTACAAACAGTGCAAACCTAACGGGACTTCACTACCCACAAGGGGAGGCTGGACAGAGCCATCGGGCCCAGAGGCTGTGAACGTGAGCTTGGCCTTTGGGCCTGTGTCTGGGAGCCGGTGTTCACAGAAGCCCTTTGTGCAGCACAGATGGAGATGTGGGGAGGTGTTTACCATTCCTGGGCCCAGGGCAGGCTCACTTTAGGGATTCCTGCCATTCCTCTAATCCAGAGCCTTCTCTCCACATCCAG
Seq C2 exon
GGTCCGGGAGGTGCCGCAGGCCCTAAGGGAGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092758-COL9A3:NM_001853:24
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(25.6=83.3),PF0139113=Collagen=FE(31.1=100)
A:
NA
C2:
PF0139113=Collagen=FE(14.9=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)