HsaINT0038822 @ hg19
Intron Retention
Gene
ENSG00000139219 | COL2A1
Description
collagen, type II, alpha 1 [Source:HGNC Symbol;Acc:2200]
Coordinates
chr12:48392198-48393908:-
Coord C1 exon
chr12:48393702-48393908
Coord A exon
chr12:48392215-48393701
Coord C2 exon
chr12:48392198-48392214
Length
1487 bp
Sequences
Splice sites
5' ss Seq
GTGGTTGTA
5' ss Score
-10.44
3' ss Seq
CTATATTTTTTCCCTTGCAGGGC
3' ss Score
11.69
Exon sequences
Seq C1 exon
AGGAGGCTGGCAGCTGTGTGCAGGATGGGCAGAGGTATAATGATAAGGATGTGTGGAAGCCGGAGCCCTGCCGGATCTGTGTCTGTGACACTGGGACTGTCCTCTGCGACGACATAATCTGTGAAGACGTGAAAGACTGCCTCAGCCCTGAGATCCCCTTCGGAGAGTGCTGCCCCATCTGCCCAACTGACCTCGCCACTGCCAGTG
Seq A exon
GTTGTAATTTATTTATTTCCTGTTCAACATAAATAAATTACTTGCAAGCACTGCAAACACGCTCCCATAGATGCTGGTCGTCTCTGCAAAGCAGAGGGGCTAGTTATCCATGGGACCTGGTAGCTGGGGTAGAAAGGAAAGGCCACTTCTCACTTGCAGGTTGAAACTGAGTGAACGAGCCTGAGACACTAGAGGGGTCCTTCTTTGCCCAACATCTCCAAAAACATTTGCTTCCAAGACACATGAAGGACAGATGTGATTCTACAAAAAAAAAAAAAAAAAAATCCTCTCTGAAATCATCTCTGCAAATTACTAGAGCCACTATGGAGATCAAATGCTCTGTCTGGCCAATCCACGAATTAATTCCTCCTCTGCCACCGACACCTTGTCTTCTCCTTAGAAGACTTCTATGTATGTGGTCTTCAGTGTGGAGAAAGCTCTGCCAGCTAGTGGGGAGACTGCAGGGGCAGAGGCTCCCTCTTTGAGTTATGGAACATTGGTGGTAGTTTCCTCTCTGCTATTACCTCTCTTGGAGTTGACCATTAATTCAGAAGCAAAATAATAGGAGAGGGAAGGGCTAGGCTTTGGGAGTTCTCGTGGGGACGGGTGGAGACAGAGCCCCATGTATCTGCACTGTAGTGGGTGGTTATAAACTCCCAGTTAGATCCAGTGCTGGTGGATGATATATGTGCAGGTGACCCCTTCCCAGCATTCATACAGATGTCCTATCTCCCTGCAGAGTGAGTGGGGACGCTTGTGTAGGTTTTTTGGGTAGCTCTTGCTGTCCGCTTCCTGCTGAAGTAGAGAAGGCCGTGGCAAGGGAAGTGAGAAGCTGCCTTTCCTTAACACTTCACCAACACTGGCTCCCTAATGTGCAGATTCCCAGATCCTTTCTGAGGGGCCCGTGTGAGTGAAGTGTTGATTGCCTTTACTATTTTGCTGCTACTGTGAAGGAGAGGTTATTGACTGGGGATGGCACAGGCTATGATGCTCCGATGCTCTTCATAACTCATATGCCTTGCTGTTTTTGTGTTTTTATTTGTGCTTGCTTCAAGGAGACCCAGCTCTAATGTAAGACCTTTCTAAGTACCTAACTCTTCCTCTGGGAGGGCTTGGGGTTCGGGAACGGCTCCCTACCCTGTGGGGGGAAGAGAGACTGAATCTGTGCTTTCCTTCTTGTGGCTGATTAGATCTTGAGCTCTTCATTGCCTTTTTGTGCTGCCCTTGCTCCTTTCTTTTGCATGCTGCCTGCTTTTTGAATAACAAAGTCTGGGTCACCTCCATTCCTCATGGGACCTCAGCAACCCCAGGGCCACAGTGGCCCTAACACCCCAACAGAGGGGTTCAGTGGAGTCACAGGAAGCTGCCGCCTTCCTTGATTGTGTCCTTTTACTTGTTTGATCTAATGAGTGTTTGAGTGACAAGAATAGGTATTTTTCCATCTCAAGATTCTTACCTTCTTCTTCTCTATATTTTTTCCCTTGCAG
Seq C2 exon
GGCAACCAGGACCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139219-COL2A1:NM_001844:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.057 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0009313=VWC=WD(100=80.0),PF0139113=Collagen=PU(9.1=7.1)
A:
NA
C2:
PF0139113=Collagen=FE(9.1=100)
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:
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)