HsaINT0038378 @ hg38
Intron Retention
Gene
ENSG00000108821 | COL1A1
Description
collagen type I alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2197]
Coordinates
chr17:50199556-50199947:-
Coord C1 exon
chr17:50199753-50199947
Coord A exon
chr17:50199591-50199752
Coord C2 exon
chr17:50199556-50199590
Length
162 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGG
5' ss Score
9.13
3' ss Seq
CGCGTCTCTTCGTCCCCTAGAGT
3' ss Score
9.9
Exon sequences
Seq C1 exon
TCCCACCAATCACCTGCGTACAGAACGGCCTCAGGTACCATGACCGAGACGTGTGGAAACCCGAGCCCTGCCGGATCTGCGTCTGCGACAACGGCAAGGTGTTGTGCGATGACGTGATCTGTGACGAGACCAAGAACTGCCCCGGCGCCGAAGTCCCCGAGGGCGAGTGCTGTCCCGTCTGCCCCGACGGCTCAG
Seq A exon
GTGCGGCTGCGCTCGGGGCCTGGGGCCTGGGGCCTGGGGCCTGGGGCCTGGGGCTGGGGCTGGGGGTGGTCGGCGCTCGCTGGCCCTCCGTGCTGGAGGCCTCTGCCGACGGGAGCAGCATTAGCAAACCTTGGCTCTAACGCGCGTCTCTTCGTCCCCTAG
Seq C2 exon
AGTCACCCACCGACCAAGAAACCACCGGCGTCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000108821:ENST00000225964:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.304 A=NA C2=0.917
Domain overlap (PFAM):
C1:
PF0009313=VWC=WD(100=47.5),PF0139113=Collagen=PU(33.9=16.1)
A:
NA
C2:
PF0139113=Collagen=PU(7.0=33.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCACCAATCACCTGCGTACAG
R:
CGACGCCGGTGGTTTCTTG
Band lengths:
226-388
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