HsaINT0169914 @ hg19
Intron Retention
Gene
ENSG00000041982 | TNC
Description
tenascin C [Source:HGNC Symbol;Acc:5318]
Coordinates
chr9:117808689-117810811:-
Coord C1 exon
chr9:117810539-117810811
Coord A exon
chr9:117808962-117810538
Coord C2 exon
chr9:117808689-117808961
Length
1577 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTT
5' ss Score
7.51
3' ss Seq
ACCATTTTCTCTCCCTCTAGAAG
3' ss Score
11.02
Exon sequences
Seq C1 exon
AGGCCCTGCCCCTTCTGGAAAACCTAACCATTTCCGACATTAATCCCTACGGGTTCACAGTTTCCTGGATGGCATCGGAGAATGCCTTTGACAGCTTTCTAGTAACGGTGGTGGATTCTGGGAAGCTGCTGGACCCCCAGGAATTCACACTTTCAGGAACCCAGAGGAAGCTGGAGCTTAGAGGCCTCATAACTGGCATTGGCTATGAGGTTATGGTCTCTGGCTTCACCCAAGGGCATCAAACCAAGCCCTTGAGGGCTGAGATTGTTACAG
Seq A exon
GTATTTCAAATCAAGTGAGCCATTTGTTCCTCTTCCTGGTCCCCTTCTGTGTAATCTGTCTACCGGATCGCCATGACTTTAACATCTTTGTTCACATTCCCTACTTAATCCATAAATGTAGTCTACTGTTTCACCTTCTCCCCACACTCCCTCTTGTCATATGTACTTAATGAACACTCCCCACTCCCACCCCAGAAATGAGAAGGTCGAAATATTTCTGCTTTGTATTCAAAATCCTTTAGACCTTGTCTTGTCCATAGCTCTTGTGTGCTTACCTCATATCATCGTCCCTTGTGATCAACCTGGCTGGTCCCCAGCTACATTTCAGCCTTCTCAAAAGAAATATACCAATGAGTATATTTCCAAAACGTATTTAAAACTTTTGCCATCTCAAAATCTCAACCATGATCTTAACAAACTTACCCAGTGGGCTCGTCATTGGAAAACCAAATGTGAACTTATTTTATCGGTAATCACTAATATCAGAGAGACTCTGCAACACGGACTAAATCCATAATTTTCTCAAGACTAATGATTCCTACAGAAATTAACAACGGAATAGTCAAACATCTGTGTTTCCCAAAGTCTTTCTAGAGATTACTAGCTCCACAGAATGTTCAAAGGTCCTACTCGGTGAGGAAATTCCACGTTCAAATAAGTTTGGAAAGACTGAGTTAAACAAAGTTAAAGAGGATCTTTAACTGCACGGCTTTTCAGAACACCCTAACGTGCATCATCTCCAAGAAGTACTTATCCAGGCAGTATTTTCCAAACTTATTTGACAAAGGATACTTTTTAAGGAAGAGGATCAAACAGGAATAGTTCACTGTGAGCACACTTTGGGAAACTCAGCTCTAAATCTACATTGACATTGAGTTTTGTCTAGTTAAGGCAATGCAAGATGAAACCCTGGGTCCACAGTATGTAGCACAAAAGGTTCCAACCTCAGTTCTACCATCTGAACATTTATCTAATAGTTAATAAAATAACAAGAAAGAATGCAAAAAAAAAAAAAAAAAGTCAAGGGTAGGAGCCTTCTTTAGTGAAACAGCACTAAGAACAAAGCAAAAAGACCATAACATTTTAAAAGCCATTTTGGGCAGGCTCAAGGAGAATGTAATCAGCAGTATCATCATGAGCAGCTCTACAGATCATTAATGCTGGTTTATTTGTCTTTTCAAAAAGAAAAGAAAAAGGTCTTGCAGGGGATGGGCACTCAGCCACTGGAAGACAGAGAGCAAATGTAAACAATTTACTGGCTTTGAACTTATTTAATAATATGTGGGACGGGCCAATGCTGAGTCCAGATGTGGATTTACTGAATTGCTTTTAGACAAAACTCACATATGCAAACATATGCTTGACTTGTATTGAATGTGTCTACTCCATCTTTCCCCTCTCCTGACTCTACTGGACTTGTTAATGTTGAATGATTTTATTTTTGGTATCTCAGGACACTTCTATCTCTGAAAGCCGGGGCATCACTACATATTGATACCCCTACTGGAGAGAAGATTGCACGGACTGGTAAATGATGTTGTCTTTCCTCCTTCTCCCACCATTTTCTCTCCCTCTAG
Seq C2 exon
AAGCCGAACCGGAAGTTGACAACCTTCTGGTTTCAGATGCCACCCCAGACGGTTTCCGTCTGTCCTGGACAGCTGATGAAGGGGTCTTCGACAATTTTGTTCTCAAAATCAGAGATACCAAAAAGCAGTCTGAGCCACTGGAAATAACCCTACTTGCCCCCGAACGTACCAGGGACATAACAGGTCTCAGAGAGGCTACTGAATACGAAATTGAACTCTATGGAATAAGCAAAGGAAGGCGATCCCAGACAGTCAGTGCTATAGCAACAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000041982-TNC:NM_002160:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.065 A=NA C2=0.112
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=88.0)
A:
NA
C2:
PF0004116=fn3=WD(100=88.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCTGGATGGCATCGGAGAAT
R:
CCAGTGGCTCAGACTGCTTTT
Band lengths:
352-1929
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)