HsaINT0039004 @ hg38
Intron Retention
Gene
ENSG00000134871 | COL4A2
Description
collagen type IV alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2203]
Coordinates
chr13:110503847-110504264:+
Coord C1 exon
chr13:110503847-110503993
Coord A exon
chr13:110503994-110504147
Coord C2 exon
chr13:110504148-110504264
Length
154 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGAG
5' ss Score
7.1
3' ss Seq
GCTTCTTTGGTGGCTTGCAGGTT
3' ss Score
8.73
Exon sequences
Seq C1 exon
GTGCCCCCGGGACTGTGGGAGCCCCCGGGATTGCAGGAATCCCCCAGAAGATTGCCGTCCAACCAGGGACAGTGGGTCCCCAGGGGAGGCGAGGCCCCCCTGGGGCACCGGGGGAGATGGGGCCCCAGGGCCCCCCCGGAGAACCAG
Seq A exon
GTAGAGTGCTGAGCTGGGGCCTGGAGCCCCTCGGGGCTGCCCGGGCAAGGCCAGGGCCTGCTGGCATTGCGTCCTCTTGTGTTCTCTTTGTGGATCGCCGGCCGTGCCAGGCGTGGTCAGTTTCCAGCCATAACGCTTCTTTGGTGGCTTGCAG
Seq C2 exon
GTTTCCGTGGGGCTCCAGGGAAAGCTGGGCCCCAAGGAAGAGGTGGTGTGTCTGCTGTTCCCGGCTTCCGGGGAGATGAAGGACCCATAGGCCACCAGGGGCCGATTGGCCAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000134871:ENST00000360467:44
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(24.6=32.0),PF0139113=Collagen=PU(58.5=62.0),PF0139113=Collagen=PU(10.8=18.0)
A:
NA
C2:
PF0139113=Collagen=PD(39.6=52.5),PF0139113=Collagen=PU(62.1=90.0)
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:
CCCCGGGATTGCAGGAATC
R:
CCAATCGGCCCCTGGTGG
Band lengths:
234-388
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