HsaINT0038940 @ hg38
Intron Retention
Gene
ENSG00000187498 | COL4A1
Description
collagen type IV alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2202]
Coordinates
chr13:110177842-110178231:-
Coord C1 exon
chr13:110178064-110178231
Coord A exon
chr13:110177932-110178063
Coord C2 exon
chr13:110177842-110177931
Length
132 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
GTCCTTTCCTTTGGCCACAGGTT
3' ss Score
9.65
Exon sequences
Seq C1 exon
GCCCTCCTGGAATAAAAGGAGAGAAGGGTTTCCCCGGATTCCCTGGACTGGACATGCCGGGCCCTAAAGGAGATAAAGGGGCTCAAGGACTCCCTGGCATAACGGGACAGTCGGGGCTCCCTGGCCTTCCTGGACAGCAGGGGGCTCCTGGGATTCCTGGGTTTCCAG
Seq A exon
GTAAGTGATTTTTGAACTTCTGCCTGGATCCATCATGAAGACATGGGCCTCACCTTATTCTTTTTATGACTCAGCATTTACTGTCAGCATTCAGAGCAAGAAAATGTTCACAGTCCTTTCCTTTGGCCACAG
Seq C2 exon
GTTCCAAGGGAGAAATGGGCGTCATGGGGACCCCCGGGCAGCCGGGCTCACCAGGACCAGTGGGTGCTCCTGGATTACCGGGTGAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000187498:ENST00000375820:32
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(31.0=31.6),PF0139113=Collagen=PU(65.0=68.4)
A:
NA
C2:
PF0139113=Collagen=PD(33.3=64.5),PF0139113=Collagen=PU(40.0=77.4)
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:
TCCTGGAATAAAAGGAGAGAAGGGT
R:
GGTAATCCAGGAGCACCCACT
Band lengths:
243-375
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