HsaINT0038880 @ hg38
Intron Retention
Gene
ENSG00000168542 | COL3A1
Description
collagen type III alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2201]
Coordinates
chr2:188996125-188996496:+
Coord C1 exon
chr2:188996125-188996178
Coord A exon
chr2:188996179-188996397
Coord C2 exon
chr2:188996398-188996496
Length
219 bp
Sequences
Splice sites
5' ss Seq
CCCGTATGT
5' ss Score
5.55
3' ss Seq
ATGTAATTTTTTCTTATTAGGGA
3' ss Score
8
Exon sequences
Seq C1 exon
GGCATGCCCGGAAGTCCAGGAGGACCAGGAAGTGATGGGAAACCAGGGCCTCCC
Seq A exon
GTATGTACATTTTTAAAATCTCATTTTAAAAGGCCAGTTAAAATGGAATGTATATGTTGGCCTATCCTTGAGTGTGTGTGTGTGTGTGTGTGTATATATATATATGTATATGTATATCTATATATATACACACACACACACACACACACATACTATATATATAGCATGCTTTAATCTTCTCTTTATCAAACCTTTATTAATGTAATTTTTTCTTATTAG
Seq C2 exon
GGAAGTCAAGGAGAAAGTGGTCGACCAGGTCCTCCTGGGCCATCTGGTCCCCGAGGTCAGCCTGGTGTCATGGGCTTCCCCGGTCCTAAAGGAAATGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168542:ENST00000304636:23
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(3.0=11.1),PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(49.2=100),PF0139113=Collagen=PU(15.2=36.4)
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:
ATGCCCGGAAGTCCAGGAG
R:
TCATTTCCTTTAGGACCGGGGA
Band lengths:
149-368
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