HsaINT0038963 @ hg19
Intron Retention
Gene
ENSG00000187498 | COL4A1
Description
collagen, type IV, alpha 1 [Source:HGNC Symbol;Acc:2202]
Coordinates
chr13:110863994-110864269:-
Coord C1 exon
chr13:110864216-110864269
Coord A exon
chr13:110864021-110864215
Coord C2 exon
chr13:110863994-110864020
Length
195 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
ACCAAAACTTTCTTTTTTAGGGA
3' ss Score
10.33
Exon sequences
Seq C1 exon
GGGGAGAGAGGGCCGCTCGGGCCTCCTGGCTTGCCTGGTTTCGCTGGAAATCCC
Seq A exon
GTGAGTAGAGGTTATTTAGGGCAGAACTTCTTTCTTTTAGTTATGACTTCTCTCTTTTCATTCCATTTCCTTTTCTTTCTTTCTTTGCTTATGTTTTAATAACTTATATTTTATATATAATATTACATGATAACAATTTTAATGCTAATGATATTTTGAGAAAAACAAAACTAACACCAAAACTTTCTTTTTTAG
Seq C2 exon
GGACCACCAGGCTTACCAGGGATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000187498-COL4A1:NM_001845:7
Average complexity
IR-S
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(10.3=44.4),PF0139113=Collagen=FE(25.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(12.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)