HsaINT0038393 @ hg38
Intron Retention
Gene
ENSG00000108821 | COL1A1
Description
collagen type I alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2197]
Coordinates
chr17:50190543-50190924:-
Coord C1 exon
chr17:50190817-50190924
Coord A exon
chr17:50190597-50190816
Coord C2 exon
chr17:50190543-50190596
Length
220 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CTCTTGTCCCTTGCTCTCAGGGT
3' ss Score
10.31
Exon sequences
Seq C1 exon
GGTGATGCTGGTCCCAAAGGTGCTGATGGCTCTCCTGGCAAAGATGGCGTCCGTGGTCTGACTGGCCCCATTGGTCCTCCTGGCCCTGCTGGTGCCCCTGGTGACAAG
Seq A exon
GTGAGGTGGCCGCCTCCCCACCTTCTGCCCTAACACATAGCCTCCTCAGCAGGCCTGGGCACGGTTCCGTGGGGTTGCGTTGGGAGAGCAGGTCCTGCCAAACTGAGCTGTCAACCTGGGAACCTGGAGGGACCAGAAGGAGGGGAGGCTCTCCTGGGGTCATCTACTAGGAGTATTCAGGGGAGGCCCTGACCCTGAGCCTCTTGTCCCTTGCTCTCAG
Seq C2 exon
GGTGAAAGTGGTCCCAGCGGCCCTGCTGGTCCCACTGGAGCTCGTGGTGCCCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108821:ENST00000225964:33
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=FE(46.7=100),PF0139113=Collagen=PU(3.3=5.6)
A:
NA
C2:
PF0139113=Collagen=PD(10.7=44.4),PF0139113=Collagen=FE(28.3=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:
GTGATGCTGGTCCCAAAGGTG
R:
GCACCACGAGCTCCAGTG
Band lengths:
157-377
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