HsaINT0169916 @ hg19
Intron Retention
Gene
ENSG00000041982 | TNC
Description
tenascin C [Source:HGNC Symbol;Acc:5318]
Coordinates
chr9:117803220-117804620:-
Coord C1 exon
chr9:117804498-117804620
Coord A exon
chr9:117803364-117804497
Coord C2 exon
chr9:117803220-117803363
Length
1134 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGA
5' ss Score
8.24
3' ss Seq
TTGCTTTTACTGTGTTCCAGGTA
3' ss Score
10.86
Exon sequences
Seq C1 exon
CCATGGGCTCCCCAAAGGAAGTCATTTTCTCAGACATCACTGAAAATTCGGCTACTGTCAGCTGGAGGGCACCCACAGCCCAAGTGGAGAGCTTCCGGATTACCTATGTGCCCATTACAGGAG
Seq A exon
GTAGGAGACTCGGAAAGGGGAGAGAGAGGAGGAGTGTTGTGGGTTTGGATGGATTCATGAAAAAGACCCTGATAATTTTCATCCTCTAACATCATGATCAAAGAAAATGAATTCTTTATTTGTGAGACCATCTGGAGAGAAGAGAACTCATTTGTAAAGTGCTATGAGGTTCTTAGAAGAAACTTTCTTGTGAAGGGTCACTTGAACAAGACCTTTTTTAACCTTGAAATTATAAAATTCTATGAGAAATAGATCTCTAGTATTGTTTGCACACAATGGCAAAAGATTCTAAATATATTGGCATTTCTCTCCCTGCGCACACTCATCTGAAAAGCTAGTCTTGGATATATGTGAAGTTTTACCTTTGGGTACCAAATCTGTCTGTCTCAGCAAATGATGGCAAGCTGTGCCTTAGAAAATTTGTGAGTTCTAACTCAAAGCGCATGGGCTATAATAGAGACCACAAGGAGGAAGCCCAGTCAAATCTGCCTAAAGACACTCTGGCAGGTAGTAAGCTACCTGTTGCTGAAAGTGTATAAAGAGAGGATGGTTAATAACCTCTTCACAGGAATGCTGTTTTGTCTCTATAGGAAGTCTGACCAGCTGATGTGCAAGTTCTTCACTAGCCCCCAAATTCTAAGAAATACAATTTCTGTGTTTATTAATAAACACTGCAGCACAAACTTGACTATAATCAACTTTCTTTTCTTAAGTAGAATTTCCTCTAGTAAGGGAGTCTATAATCCTAAGCCAAGACAATGGGTGCAATAGATCTGACATACATTACATAGTAAGCTTCCCATATTGTTTGTGGGGAAAAATAATAAGATAAAATTTGCACAACGTGCCAGCTCTCTACTGAACGGAAACTTGCCATTTTTAGTACGTTGTGACTTCATGTTTTCCCCCGCCCCTCCTGGCTTTGTTTTTGGCATCTGCACCAATAGAAAAAGCATACAAAAAGTAAGCCTTCTTCCCTTATGCCAGAGGGTAGGAGCAAATGAGAAGTCAAGAAAGTGGTGTTTGATGAAGATATAGTTTCATTTCTAAATCAGATACACTCTTTTTGGGGGCAACAGTGAATAAGTGTCAGTGAGGTTCATTATTCCTCATCTTGCTTTTACTGTGTTCCAG
Seq C2 exon
GTACACCCTCCATGGTAACTGTGGACGGAACCAAGACTCAGACCAGGCTGGTGAAACTCATACCTGGCGTGGAGTACCTTGTCAGCATCATCGCCATGAAGGGCTTTGAGGAAAGTGAACCTGTCTCAGGGTCATTCACCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000041982-TNC:NM_002160:18
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.195
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(48.8=92.9)
A:
NA
C2:
PF0004116=fn3=PD(50.0=81.6),PF106044=Polyketide_cyc2=PU(4.2=14.3)
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:
GGCTCCCCAAAGGAAGTCATT
R:
CTGTGGTGAATGACCCTGAGAC
Band lengths:
262-1396
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)