HsaINT0169931 @ hg19
Intron Retention
Gene
ENSG00000041982 | TNC
Description
tenascin C [Source:HGNC Symbol;Acc:5318]
Coordinates
chr9:117838669-117840491:-
Coord C1 exon
chr9:117840222-117840491
Coord A exon
chr9:117838855-117840221
Coord C2 exon
chr9:117838669-117838854
Length
1367 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
ATGTTCCTTCTCTCAAACAGGCC
3' ss Score
10.59
Exon sequences
Seq C1 exon
GCTTGGATGCCCCCAGCCAGATCGAGGTGAAAGATGTCACAGACACCACTGCCTTGATCACCTGGTTCAAGCCCCTGGCTGAGATCGATGGCATTGAGCTGACCTACGGCATCAAAGACGTGCCAGGAGACCGTACCACCATCGATCTCACAGAGGACGAGAACCAGTACTCCATCGGGAACCTGAAGCCTGACACTGAGTACGAGGTGTCCCTCATCTCCCGCAGAGGTGACATGTCAAGCAACCCAGCCAAAGAGACCTTCACAACAG
Seq A exon
GTAAAAGGCCTCCCCCTGTTAACAGATATAGTAAAGGAAAGATTGAAAGATTTCCATCCCACTCCATGTTGGGGTATCTTCCAGGCTCATTTTACAGTACGAAAAATGAAAGGGGTATTTCTACTCCTGTAAATTTTAAAATATTGTAGCAATTTATTAATTAATTTTTCAAAAAAAATTCCAAATAACCTTCCAAAGCACTTTTGGGGGTGGGGGACATATGTAGAAGATGCTGGTCTGATATTCTCAGACAAAAGTTCTGGTTAAAATAAAGTTCAAATAAATATTTTTAAAGTAAAATATGGTATATGGAAAACATATATGACAAATGAGCCTCCTAACACTTTAGCCTACGGCATTATTTTAAAAGTTCAAAAGTGTCAATTTTTCATTCAGTAAATATTTTTCAGAGCTCAGTAAGTACTTTGTGAGTTATTAGAAATATGATGAGGAGGCCGGGCGTGGTGGCTCACGCCTGTAATCCCAGCACTTGGCAGGCTGATGCAGGCAGATCATGAGGTCAAGAGATGGAGACCATCCTGGCCAACATGGCAAAACCCTGTCTCTACTAAAAGTACAAAAATTGGGGTCAGGCGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCGGGCGAATCACGAGGTCAGGAGATTGAGACCATTCTGGCTAACACAGTGAAACCCCGTCTCTACTAAAAATACAAAAAAAATTAGCCAGGCGTGGTGGCGGGTGCCTGTAGTCCCAGCTACAGGCTGAGGCAGGAGAATGGCATGAACCCAGGAGGTGGAGCTTGCAGTGAGCCGAGATCGCACCACTGCATTCCAACCTGGGTGAAGAGCGAGACTCCGTCTCAAAAAAATAAATAAATAACTGGGCGTGGTGGTGTGCTCCTGCAATCCCAGGTACTCGGGAGGCTGAGGCAGGAGAATCACTTGAACCTGGGAAGCAGGGGTTGCAGTGAGCCGAGATCGCACCAACACACTCCAGCCTGGTGACAGAGCGAGACTCTTGTCTCAAAAAAATAAAATAAAGAATGAAATATGATGAGAAAATGCAAAAGACCAGTTTTTACACTCATGAGCTTATTTTTAAGTCTTTGCATTGTTTCTTTAACCACAAAGTCTGAGAAAAACACAAATGACTAAAGTGTCGCACTCATCCATAATAGGGAAAGGTGCCAAATCTGTAGCACTTGTTTAGATTTGCACATCCACTATGGGGACAGATGAGTGTGCTGAGAATTTTGTAATTTCTCTCCAGTTCCAGGCACGTTTCATATGTCAGCTTGAGCTGTCAAAGACTCCTGCTCTCTTGTGACTGATATGTTCAATACAAATGTTCCTTCTCTCAAACAG
Seq C2 exon
GCCTCGATGCTCCCAGGAATCTTCGACGTGTTTCCCAGACAGATAACAGCATCACCCTGGAATGGAGGAATGGCAAGGCAGCTATTGACAGTTACAGAATTAAGTATGCCCCCATCTCTGGAGGGGACCACGCTGAGGTTGATGTTCCAAAGAGCCAACAAGCCACAACCAAAACCACACTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000041982-TNC:NM_002160:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.505 A=NA C2=0.566
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=89.0)
A:
NA
C2:
PF0004116=fn3=PU(71.4=95.2)
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:
CCAGCCAGATCGAGGTGAAAG
R:
ACTGTCAATAGCTGCCTTGCC
Band lengths:
350-1717
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)