HsaINT0038876 @ hg19
Intron Retention
Gene
ENSG00000168542 | COL3A1
Description
collagen, type III, alpha 1 [Source:HGNC Symbol;Acc:2201]
Coordinates
chr2:189849486-189849973:+
Coord C1 exon
chr2:189849486-189849688
Coord A exon
chr2:189849689-189849922
Coord C2 exon
chr2:189849923-189849973
Length
234 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
GTTTCTTTTCCATTTATTAGCCT
3' ss Score
4.9
Exon sequences
Seq C1 exon
CTGTTGAAGGAGGATGTTCCCATCTTGGTCAGTCCTATGCGGATAGAGATGTCTGGAAGCCAGAACCATGCCAAATATGTGTCTGTGACTCAGGATCCGTTCTCTGCGATGACATAATATGTGACGATCAAGAATTAGACTGCCCCAACCCAGAAATTCCATTTGGAGAATGTTGTGCAGTTTGCCCACAGCCTCCAACTGCT
Seq A exon
GTGAGTTTAAAGATAAACTGTACATCTTCAATATTCATATTTAGACACATGAATAGCTCCTATATCATAGGAGCCTAAAAGGGAATGAAAGTCATGTTCATCAAATAGCCATGTTTGTATTACGAGTAAAAAGTGACCGTTTCAATTTAAAGATAAGGATTGGTTAGAATCTGGGTTACTAAATAATATGCAAATTCTGTGTCTTGTTTAACTTGTTTCTTTTCCATTTATTAG
Seq C2 exon
CCTACTCGCCCTCCTAATGGTCAAGGACCTCAAGGCCCCAAGGGAGATCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168542-COL3A1:NM_000090:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0009313=VWC=WD(100=83.8)
A:
NA
C2:
PF0139113=Collagen=PU(27.8=88.2)
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:
CTGTTGAAGGAGGATGTTCCCA
R:
GATCTCCCTTGGGGCCTTGAG
Band lengths:
252-486
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)