HsaINT0038375 @ hg19
Intron Retention
Gene
ENSG00000108821 | COL1A1
Description
collagen, type I, alpha 1 [Source:HGNC Symbol;Acc:2197]
Coordinates
chr17:48272795-48273026:-
Coord C1 exon
chr17:48272928-48273026
Coord A exon
chr17:48272840-48272927
Coord C2 exon
chr17:48272795-48272839
Length
88 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGT
5' ss Score
8.56
3' ss Seq
CTCCTTTCTCTGTGCCACAGGGA
3' ss Score
9.83
Exon sequences
Seq C1 exon
GGTGAAGCTGGTCCCCAAGGGCCCCGAGGCTCTGAAGGTCCCCAGGGTGTGCGTGGTGAGCCTGGCCCCCCTGGCCCTGCTGGTGCTGCTGGCCCTGCT
Seq A exon
GTAAGTGTCCCCGACTCAGTGTCCCCTTTGCCACTTTCTAACCTCAGAGTCCTTGCCTGTTGCTGACACTCCTTTCTCTGTGCCACAG
Seq C2 exon
GGAAACCCTGGTGCTGATGGACAGCCTGGTGCTAAAGGTGCCAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108821-COL1A1:NM_000088:17
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(3.3=6.1),PF0139113=Collagen=PU(48.3=87.9)
A:
NA
C2:
PF0139113=Collagen=FE(23.3=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:
GTGAAGCTGGTCCCCAAGG
R:
ATTGGCACCTTTAGCACCAGG
Band lengths:
143-231
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)