HsaINT0169932 @ hg19
Intron Retention
Gene
ENSG00000041982 | TNC
Description
tenascin C [Source:HGNC Symbol;Acc:5318]
Coordinates
chr9:117838311-117838854:-
Coord C1 exon
chr9:117838669-117838854
Coord A exon
chr9:117838401-117838668
Coord C2 exon
chr9:117838311-117838400
Length
268 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CTTGCACATTCTCTCCTTAGGTC
3' ss Score
11.62
Exon sequences
Seq C1 exon
GCCTCGATGCTCCCAGGAATCTTCGACGTGTTTCCCAGACAGATAACAGCATCACCCTGGAATGGAGGAATGGCAAGGCAGCTATTGACAGTTACAGAATTAAGTATGCCCCCATCTCTGGAGGGGACCACGCTGAGGTTGATGTTCCAAAGAGCCAACAAGCCACAACCAAAACCACACTCACAG
Seq A exon
GTGAGCTCTGCATCTCTGCAAGCCTGAGCCAGCCAGCCCTAGAGGGCCCTTAAAGGATGGGCACCTGCTCCCACATGTCCCCATTTGCAACCCTCAGAAATAAGTCCAATTTCCTGAAATACTGCTTATTGGATTGCAGTGAGTTCTTTTGTAAAACATTCCGAAAATTTGTTGTAGCCTCCAGAGACCAACTCAAAGCCATTTTTATCATCCTCTGAAAGTCTCTCTGATTTCAGGATGAATCTCAACTTGCACATTCTCTCCTTAG
Seq C2 exon
GTCTGAGGCCGGGAACTGAATATGGGATTGGAGTTTCTGCTGTGAAGGAAGACAAGGAGAGCAATCCAGCGACCATCAACGCAGCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000041982-TNC:NM_002160:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.566 A=NA C2=0.839
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(71.4=95.2)
A:
NA
C2:
PF0004116=fn3=PD(27.4=74.2)
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:
GCCTCGATGCTCCCAGGAATC
R:
CTGTGGCTGCGTTGATGGTC
Band lengths:
276-544
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
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)