HsaINT0039832 @ hg19
Intron Retention
Gene
ENSG00000092758 | COL9A3
Description
collagen, type IX, alpha 3 [Source:HGNC Symbol;Acc:2219]
Coordinates
chr20:61468435-61470113:+
Coord C1 exon
chr20:61468435-61468617
Coord A exon
chr20:61468618-61470035
Coord C2 exon
chr20:61470036-61470113
Length
1418 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
GTGTCCACACCTCGTGACAGGAA
3' ss Score
4.84
Exon sequences
Seq C1 exon
AACAAATTGCACAGTTAGCCGCGCACCTAAGGAAGCCTTTGGCACCCGGGTCCATTGGTCGGCCCGGTCCAGCTGGCCCCCCTGGGCCCCCAGGACCCCCAGGCTCCATTGGTCACCCTGGCGCTCGAGGACCCCCTGGATACCGCGGTCCCACTGGGGAGCTGGGAGACCCCGGGCCCAGAG
Seq A exon
GTGAGTGTTTGACCCCATGACACGGTCACCCTGCTGTAAAAATCCCTGAGACTGACTTGTTAGTAGGCGCTGCTTCTGGTGCCTGCCATGCGCCCTCAGGGGTAACCCCTGGAACGTGGGGGCCTCTCATGTTTTGGGGCCTAGCGCAGTTAACTCCTTGGTAATCCTGTGGGAACTGGAACATTTTTAACATGTGATGTTTTTCTCAAATACCATTAGAACAATATTTGGCAGGGAGGGATTGATTTAAAATGTGACGAAGGCTGGGCGCGGTGGCTCACGCCTGTAATCCCAACACTTTGGGGGGCTGAGGTGGGCAGATCACGAGGTCGGGAGTTCAAGACCAGCCTGACCAACATGGTGAAACCCTGTCTCTACTAAAAATACAAAAATTAGCTGGGCATGGTGGCACACGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCTCTTGAACCCTGAAGGCAGAGGTTGCAGCGAGCTGAGATCGCACCATTGCACTCCAGCTTGGGCGACAGAGCGAGACTCCGTCTCCATAAAAGAAAAAAAAAATGTGAGGAATGGCCGGGTGCGGTGGCTCATGCCTGTAATCCCAGCACGTTGGGAGGACGAGGCAGGTGGATTACTGGAAGTCAGGAGTTCAAGACCAGCCTGGTCAACATGGTGAAACCCCGCCTCTACTAAAAATACAAAATTAGCCAGGCAAAACACAGATGTAAGATTTGAATGACGCAATTAGAGGGATGTGAAAATGCCCTTAGGTGAACCATGGGTGGAAAATCATTTAAAACATGATTACAAAATATTAATAAATACTCAACTGCTTAATAGGCATAAATATTTTGAACAAAACTAAAATCCCATTTAAATTGGCTGCCAGAGGTCAGGGAGGTGGTTCAGCCGTGCACGGCTCAGCAGCAGGCATAGGTTCTGACGGCTGTGCCACTGGGCGGTTTCACTGTGGAACATCTGAGTTCACTTACGCAAGCCCGGCCTCCTGCACCCCTGGGCCGTGTGCCAGAGCCTGGGGTTTATGGCTGCAGACCTGCACAGCCTGTTACTGGGCTGGGTCTTGTGGGCGGTTCTAACCTGGTGGTGGGTATCTGTGTTAAATACATCCAAACACGGGAAAGGAATGGTAAAAATTGGGTATGATAATCTTAAGGGACCACTGTCACCTATGCGGTGCGTCGTCCACCTGCAGCCGTCCTGCAGTCTAAGACTGTGTACAGGTGGGTCCCTCTCGTCGGACCCCGTCAAGCCCTACGCGTGTGACATCTGTACTTTTCTAAATGTTTCCACTTCAGTGAAAAGCTGGCACCCTGTTTGTTACAAAGGTTGATCAGACACCGCTGTGGTGTGGCTGCAACAGATACTCTAACCATATGTCTGTGTCCACACCTCGTGACAG
Seq C2 exon
GAAACCAGGGTGACAGAGGAGACAAAGGCGCGGCAGGAGCAGGGCTGGACGGGCCTGAAGGAGACCAGGGGCCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092758-COL9A3:NM_001853:30
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=PU(75.8=75.8)
A:
NA
C2:
PF0139113=Collagen=PD(22.6=51.9),PF0139113=Collagen=PU(23.8=55.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAATTGCACAGTTAGCCGCG
R:
GGCCCCTGGTCTCCTTCAG
Band lengths:
254-1672
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)