HsaINT0038426 @ hg38
Intron Retention
Gene
ENSG00000164692 | COL1A2
Description
collagen type I alpha 2 chain [Source:HGNC Symbol;Acc:HGNC:2198]
Coordinates
chr7:94409564-94409821:+
Coord C1 exon
chr7:94409564-94409608
Coord A exon
chr7:94409609-94409722
Coord C2 exon
chr7:94409723-94409821
Length
114 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
CACTGCATTTTCCTTCACAGGGC
3' ss Score
10.41
Exon sequences
Seq C1 exon
GGTAATCCTGGAGCAAACGGCCTTACTGGTGCCAAGGGTGCTGCT
Seq A exon
GTGAGTATACCTGCGTAGCTAAAATGTGCTGCTATGATTTTAAAGGCATTTAATGTGTGCTGCCTCTACAGCCCATCACCTCCCTAATGGACCACACTGCATTTTCCTTCACAG
Seq C2 exon
GGCCTTCCCGGCGTTGCTGGGGCTCCCGGCCTCCCTGGACCCCGCGGTATTCCTGGCCCTGTTGGTGCTGCCGGTGCTACTGGTGCCAGAGGACTTGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000164692:ENST00000297268:18
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(16.5=100)
A:
NA
C2:
PF0139113=Collagen=PD(14.1=36.4)
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:
GTAATCCTGGAGCAAACGGCC
R:
ACAAGTCCTCTGGCACCAGTA
Band lengths:
142-256
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