HsaINT0038862 @ hg19
Intron Retention
Gene
ENSG00000139219 | COL2A1
Description
collagen, type II, alpha 1 [Source:HGNC Symbol;Acc:2200]
Coordinates
chr12:48389658-48390408:-
Coord C1 exon
chr12:48390331-48390408
Coord A exon
chr12:48389703-48390330
Coord C2 exon
chr12:48389658-48389702
Length
628 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
CATTTTCTGTTCCGATGCAGGGC
3' ss Score
9.2
Exon sequences
Seq C1 exon
AACTTTGCTGCCCAGATGGCTGGAGGATTTGATGAAAAGGCTGGTGGCGCCCAGTTGGGAGTAATGCAAGGACCAATG
Seq A exon
GTAAGAAAAGACACTAGTTCTTTGCAGCCAAAATGGCAGGAGGTGGCCCTTAGCAGAGCCAGAGAGTCTGACAACCTCTGCTTTACAGATAATTGCTTAGAGTGGCTCTCCTCCGTAGTTATGTAACCTCCCATTCAGCTAGCCCAAAGCATTTGGTTTTTAATGGCAATGGATGCCACTTTTAATGATGCGCTGGAGTGACTAAGAAGAATGAAGATGGGGAGATGCATATAGGCTGATCTGTTAGAAGACCAGTTGCTATTGCTCTTGGAATGAGAACTGAAGAATGCAGACAGCAGCTACTGTTCTCCAGCATCCACAGACTTCCAGCAGGAAATCTCAGCCCGCAGCTCTGACTTGGCACATGCTAAATGAAACTCAGCCTTTAGTAAACATGGCTGCTGTCCAGGAGAAAGCAAGGCCAGCTTTTCTGTCCAAATGGTGCCTATAAATAAAAATAGAGTGTTGCGTGGGGAGTGGGAAATGAGAGGGAGCAGCCACTCTAGGCCCCTTGCCCACAGAGTAACTTCTTGTCCTTTGCCCGGGCTGTTGGCTGGGAGAAGATGGCACACTGGAGGCCACTGAGGAAGCATGTGTAGTAAACCCCTCATTTTCTGTTCCGATGCAG
Seq C2 exon
GGCCCCATGGGACCTCGAGGACCTCCAGGCCCTGCAGGTGCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139219-COL2A1:NM_001844:8
Average complexity
IR-S
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=PD(6.1=15.4),PF0139113=Collagen=PU(6.5=15.4)
A:
NA
C2:
PF0139113=Collagen=FE(22.6=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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)