HsaINT0038776 @ hg19
Intron Retention
Gene
ENSG00000196739 | COL27A1
Description
collagen, type XXVII, alpha 1 [Source:HGNC Symbol;Acc:22986]
Coordinates
chr9:116968039-116968576:+
Coord C1 exon
chr9:116968039-116968092
Coord A exon
chr9:116968093-116968531
Coord C2 exon
chr9:116968532-116968576
Length
439 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCAG
5' ss Score
4.95
3' ss Seq
CTCTGTGTTTTGTGTTTCAGGGG
3' ss Score
12.38
Exon sequences
Seq C1 exon
GGGCAGCCAGGACCTGAGGGCAGCCCAGGGGCCAAAGGTTACCCTGGCAGGCAG
Seq A exon
GTGCAGTATATGGCTTCTGGAAGCTCTGTGGCCATGGTGATGTGAAGATGGCCACAGGTGCCCCGAGGCAGAGGGAGGTGGTGGGCTGGGGGCCAAGGAGCTGCACCTGCTGGGTGGACCCTAAGGAGGGGGCTTTCCAGGGGACTGGACCAAGGAAGCCTGTCTTTGCAGGCACAGGATAAGGCTGCATAGTAAGAGGAGGTCTGGTTCTGCGGGGCTGGGGCTCCAGAGGCTCCTCCTACTCAGTCTCCCTCCTACCCACCAGCCACCTCCCTGGGATCCTAGGGCTGTGGGGGTCAGGCCAAAGATCGCTGATCTAACCCCACCCCCATTCTACAAAGAGAGCAGCAGAGGCCCCAAAGAGGCAGGACTTGCCCCAGGATTGGCAGCAGGTAGAGCGTCTCCATATGTCCTTGCCCCTCTGTGTTTTGTGTTTCAG
Seq C2 exon
GGGTTACCTGGACCGGTAGGAGATCCCGGCCCCAAAGGCAGCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196739-COL27A1:NM_032888:9
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=FE(25.8=100),PF0139113=Collagen=FE(22.1=100),PF0139113=Collagen=PU(11.6=44.4)
A:
NA
C2:
PF0139113=Collagen=PD(5.7=33.3),PF0139113=Collagen=FE(18.4=100),PF0139113=Collagen=PU(17.5=73.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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
- 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)