HsaINT0038822 @ hg38
Intron Retention
Gene
ENSG00000139219 | COL2A1
Description
collagen type II alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2200]
Coordinates
chr12:47998415-48000125:-
Coord C1 exon
chr12:47999919-48000125
Coord A exon
chr12:47998432-47999918
Coord C2 exon
chr12:47998415-47998431
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:ENST00000380518:2
Average complexity
IR
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