Special

HsaINT0038385 @ hg38

Intron Retention

Gene
ENSG00000108821 | COL1A1
Description
collagen type I alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2197]
Coordinates
chr17:50192797-50193047:-
Coord C1 exon
chr17:50192994-50193047
Coord A exon
chr17:50192851-50192993
Coord C2 exon
chr17:50192797-50192850
Length
143 bp
Sequences
Splice sites
5' ss Seq
GTCGTAAGT
5' ss Score
9.9
3' ss Seq
CCTTTGCTCTCTCCCTGCAGGGT
3' ss Score
13.83
Exon sequences
Seq C1 exon
GGAGAGCCCGGCAAGGCTGGAGAGCGAGGTGTTCCCGGACCCCCTGGCGCTGTC
Seq A exon
GTAAGTATCTCCTTTCCATCCCTACCTCCTTCCCATTGCTGCCCCGGCACTTTCTCCTCCCTGCAGGAGGGGTGCTAGAGGCCACGGTCCTCAGCTGCTCGGGGCCTCCTAACCCTGAGTTCCCCTTTGCTCTCTCCCTGCAG
Seq C2 exon
GGTCCTGCTGGCAAAGATGGAGAGGCTGGAGCTCAGGGACCCCCTGGCCCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108821:ENST00000225964:26
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


Main Skipping Isoform:


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:
GCTGGAGAGCGAGGTGTTC
R:
GGGGTCCCTGAGCTCCAG
Band lengths:
82-225
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