HsaINT0039835 @ hg38
Intron Retention
Gene
ENSG00000092758 | COL9A3
Description
collagen type IX alpha 3 chain [Source:HGNC Symbol;Acc:HGNC:2219]
Coordinates
chr20:62819929-62821216:+
Coord C1 exon
chr20:62819929-62819982
Coord A exon
chr20:62819983-62821180
Coord C2 exon
chr20:62821181-62821216
Length
1198 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGT
5' ss Score
10.75
3' ss Seq
CGCCTGCTTTCCTCCCACAGGGA
3' ss Score
12.38
Exon sequences
Seq C1 exon
GGTCTGACTGGACGAGATGGACCCCCTGGACCCAAGGGTGCCCCTGGGGAACGG
Seq A exon
GTAAGTGCCTGCGCCGAACCCAGTGGCTTGGGTTCAGAGGTGAGGTCCCCTGGCCACCTCTGGCTGCTCTGTGTCCACAAGGCCAAGGAGCTGGTAGTTCCAAGGACAGCTGCCCTGCCCGTGCCTGGGGTGGAGGGGCAGAAGGGCAGGGTGCCAAGTGGCCAGTCCCCTGTGCCTGCCTCCCTGCCTCACCTCCACGTATGGTCAGAGTTGTCCTGGTATCCAGACCATGGCAGGGAGAAGGGGGATGGTTTGGGGGAACCCACCCCAGGTGCCTCCTCAGAATGTCCCTGAAGCCCCCAGGGCCCTGGGCAGACCACCACCAGGGACCCCCGGGCACGCAGCCTGCAGAGTCCCCTGTGCCTGCCTGTTGGACACTGAATCCTTTACCCTGACGGAGCGGCACCACCACCCAAGGGTGCCTTTCTCCCCTTGTGGCTTCTGAGTACAAACCCGAAGCCAGCATTCTCTCTTTGGCTTCATAAGACGTGGCTGTCAGCCAACCGGGTGCCACTGGCCCCAGGCGCAAAGCATCACAGAGGGCAGGAAGGCTGGGCTGGGGACACGAGGACACAGCCCTGCCCTTGGGACCCTTGGGAGCTCGTCAGGCATGAGGCGGATTCTGAGCTGAAAACAGGAGGGAAACAGTAGCTGCTGGCAGCCGAGTCCGTGGTGCCCAGGGGTGTGGGGTGGGCTGGTCCCCAGGCTTTCAGGAGGGGCCTCCAGCCTCAGCACAGGGCCCGTGCGTGCCGTCCAGGGAATGAGGCATTTCAGGCAGCAGGGGCCAGACAGGGCCCAGAGGGTGTGGAGGGCAGACAGGGCCTGGCTGCCCAAGGCTCTGGGGCTCGCTGACGTGGGCGGGGGCTGAGGACTCAGCAGGCTCCGTGGGTGGGTTATCGGGAGGGCTTCCTGGTGGAGACAGGCACCCCGGGTCACTTCGGTGCCTCTCAGCCCTGCCTCAGGTTGCACCTTCTTGCAGCGAGCGCTGGGACTCTGGTGCCATCTGTCTCCAGCAGCTCCCCAGGACGGCAAAGACCCTCCAGGTCAAGAGGGCTCAGAGGCCCTGCCCCTCTGTGAAGTGGGGACTTGGACCCTGTTGTCCTGGGAGTTGGAGTTGTGACGTCACACTTCAGAGGGAGGGGATTGGGTTTGCAAATAGAGGCCCAGCCCAACCTAGACGCCTGCTTTCCTCCCACAG
Seq C2 exon
GGAAGTCTGGGACCCCCGGGGCCGCCCGGGCTGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092758:ENST00000343916:5
Average complexity
IR
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(0.1=0.0),PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(19.3=100),PF0139113=Collagen=PU(1.8=8.3)
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:
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
- Autistic and control brains
- Pre-implantation embryo development