HsaINT0038840 @ hg38
Intron Retention
Gene
ENSG00000139219 | COL2A1
Description
collagen type II alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2200]
Coordinates
chr12:47981343-47981829:-
Coord C1 exon
chr12:47981776-47981829
Coord A exon
chr12:47981397-47981775
Coord C2 exon
chr12:47981343-47981396
Length
379 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
CCTCCCTTCCCCACCCTCAGGGA
3' ss Score
10.81
Exon sequences
Seq C1 exon
GGCCTGACAGGTCCCATTGGCCCCCCTGGCCCAGCTGGTGCTAATGGCGAGAAG
Seq A exon
GTGAGTCCCGGCTCCTTTCCTCTCCACACCTTGCCTCCCTGTCACACCTCCTTCTTATCTCCTGCCAAAGGCGGTTCTGTCTTGTCCTCCCTCACCACTGTCACCCTCGGCCAAGGCCGTAGGAGTGAAGAGGGGGCCCTCTCAGAAGTGAAGCCGCTGGCAGTGTTCCCTGTTGGGTGGGGCAACTGGGCTGGGGTAAACACACATTCAGCAGAGGCCCTCGAGAGGGTGCGGGTATGGGCTGCACAGTAACACAGGCTGTGCCAGGGGGACCTGGAGCCCCCTTCCCACGAGCAAGGCCCCCCAAATGCACTTTGCCCTCTCCCACTCTGCCTCCCCACCTTCTTACCCCAGCTCTTCCTCCCTTCCCCACCCTCAG
Seq C2 exon
GGAGAAGTTGGACCTCCTGGTCCTGCAGGAAGTGCTGGTGCTCGTGGCGCTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139219:ENST00000380518:36
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(23.9=100),PF0139113=Collagen=PU(15.9=61.1)
A:
NA
C2:
PF0139113=Collagen=PD(5.6=22.2),PF0139113=Collagen=FE(24.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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