HsaINT0039002 @ hg38
Intron Retention
Gene
ENSG00000134871 | COL4A2
Description
collagen type IV alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2203]
Coordinates
chr13:110503121-110503481:+
Coord C1 exon
chr13:110503121-110503282
Coord A exon
chr13:110503283-110503382
Coord C2 exon
chr13:110503383-110503481
Length
100 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACA
5' ss Score
8.92
3' ss Seq
ACGTCTTGTTTGTGTTGCAGGGC
3' ss Score
10.33
Exon sequences
Seq C1 exon
GTTATCGGGGCCCACCAGGGCCACCAGGTTCTGCTGCTCTTCCTGGAAGCAAAGGTGACACAGGGAACCCAGGAGCTCCAGGAACCCCAGGGACCAAAGGATGGGCCGGGGACTCCGGGCCCCAGGGCAGGCCTGGTGTGTTTGGTCTCCCAGGAGAAAAAG
Seq A exon
GTAACAGTGCCCATGGCCATGGGCCAGCAGCCCTGGCCACAGTGAGAGGAGCCCCCTCCCCACAGACTTTCGTGTCCCTAACGTCTTGTTTGTGTTGCAG
Seq C2 exon
GGCCCAGGGGTGAACAAGGCTTCATGGGGAACACTGGACCCACTGGGGCGGTGGGCGACAGAGGCCCCAAGGGACCCAAGGGAGACCCAGGATTCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000134871:ENST00000360467:42
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(13.2=21.8),PF0139113=Collagen=PD(74.6=85.5),PF0139113=Collagen=PU(23.1=27.3)
A:
NA
C2:
PF0139113=Collagen=FE(50.8=100)
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:
TTATCGGGGCCCACCAGG
R:
GAATCCTGGGTCTCCCTTGGG
Band lengths:
256-356
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