HsaINT0037970 @ hg38
Intron Retention
Gene
ENSG00000111799 | COL12A1
Description
collagen type XII alpha 1 chain [Source:HGNC Symbol;Acc:HGNC:2188]
Coordinates
chr6:75138448-75138961:-
Coord C1 exon
chr6:75138822-75138961
Coord A exon
chr6:75138581-75138821
Coord C2 exon
chr6:75138448-75138580
Length
241 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGTT
5' ss Score
5.77
3' ss Seq
TTTTGTCCTCTTTCTCCAAGACC
3' ss Score
6.49
Exon sequences
Seq C1 exon
GACCCGTGCCAGCCCCAACAAACTTAAAGATTACTGAAGTAACATCAGAGGGTTTCAGAGGGACTTGGGATCATGGAGCTTCAGATGTGTCTCTCTACAGAATAACTTGGGCACCTTTTGGAAGCTCAGATAAGATGGAG
Seq A exon
GTAGTTAACTCTCTTTATCTTTCTCTCTGTCTTTCATGTCCCATTTAATTTGTAGGGAAGCTTAGTTCAAAGAAGTATTACTCTTGTTGTCAATAAGCATTTATTGACATTTGAGCTCATGACATGCATCAGAGCAGGAGGAACATCTGGCTAAATAATGTGAATAAACTGCCATTGAGTGTGTATGATGTAAGTGGAGACTTACTTTTGCGTGGGTATGTTTTTGTCCTCTTTCTCCAAG
Seq C2 exon
ACCATCTTAAATGGAGATGAAAACACTTTGGTGTTCGAAAACCTGAACCCCAACACCATCTATGAAGTTTCCATTACTGCCATCTATCCTGATGAGTCAGAAAGTGATGACCTGATTGGCAGTGAGCGCACAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000111799:ENST00000322507:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.323 A=NA C2=0.536
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(54.4=91.5)
A:
NA
C2:
PF0004116=fn3=PD(43.0=75.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCCAGCCCCAACAAACTTA
R:
GTGTGCGCTCACTGCCAATC
Band lengths:
268-509
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