HsaINT0038383 @ hg38
Intron Retention
Gene
ENSG00000108821 | COL1A1
Description
collagen type I alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2197]
Coordinates
chr17:50193943-50194183:-
Coord C1 exon
chr17:50194130-50194183
Coord A exon
chr17:50194042-50194129
Coord C2 exon
chr17:50193943-50194041
Length
88 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
TTCGTGCCTCCCATCCTTAGGGT
3' ss Score
10.84
Exon sequences
Seq C1 exon
GGTCTGACTGGAAGCCCTGGCAGCCCTGGTCCTGATGGCAAAACTGGCCCCCCT
Seq A exon
GTAAGTATCACTCCCCCTGAACCCCCTGCCATTGTCCTGTCTGCCTCCCTGCTGTCCTCACTGCTGCTTTCGTGCCTCCCATCCTTAG
Seq C2 exon
GGTCCCGCCGGTCAAGATGGTCGCCCCGGACCCCCAGGCCCACCTGGTGCCCGTGGTCAGGCTGGTGTGATGGGATTCCCTGGACCTAAAGGTGCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108821:ENST00000225964:24
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:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCTGACTGGAAGCCCTGG
R:
CCTTTAGGTCCAGGGAATCCC
Band lengths:
146-234
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