HsaINT0173477 @ hg19
Intron Retention
Gene
ENSG00000165699 | TSC1
Description
tuberous sclerosis 1 [Source:HGNC Symbol;Acc:12362]
Coordinates
chr9:135800974-135802691:-
Coord C1 exon
chr9:135802588-135802691
Coord A exon
chr9:135801127-135802587
Coord C2 exon
chr9:135800974-135801126
Length
1461 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATG
5' ss Score
8.99
3' ss Seq
TTGTTCTTTTACATTTTCAGCAC
3' ss Score
9.56
Exon sequences
Seq C1 exon
ACCGTGGCCCTATGCTTGTAAACACCTTGGTGGATTATTACCTGGAAACCAGCTCTCAGCCGGCATTGCACATCCTGACCACCTTGCAAGAGCCACATGACAAG
Seq A exon
GTAATGGCTGAAATATCATAGGCATTTCATATGTTCTTCATGAGTACAACAGCTTCTGTGCACGGCCACTGTGCAACTTGTCCTGAGCTTATTCTTTTGATTTCTGTGCGCCACTGATGACATTGTTCCCAGTTTATAACTACATATAAAAATTACTTTGTAGGACCCATGATTCTTGAAAAGTTTACAAAATAAAACATATTTCAGAGACTGTTAAAGATCTTGTTTGGGCCGGGTGTGGTGGCTCACGCCTGTAATCCCCTTAGGAGGCCGAGGCGGGTGGATTGCCTGAGGTCACGAGTTTGAGACCAGCCTGGCCAACACAGTGAAACCCCGTCTCTACTAAAAAATACAAAAAATTAGCTGGGCGTGGTGGTGGACACCTATAATCTCAGCTACTCAGGAAGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGCGGAGGTTGCAGTGACCTGAGATTGCACCATTGCACTCCAGGGCAACAAGAGTGAAACTGTCTCAAAAAAAAAAAAGATCTTGTTTAAAGAAATCTTACATTTCCAGTACTATAATTGTATAGTGATGATTTGGCCCATAGGTACCCATCTTTCAACCCATACTTTGAATAGAATTTTTAGACTTTTATCGATATGGAAAAGCTTCAAGTACAAAGGACTAACATGACAAATTAATGAGTCTTGTTTCCTAGCACCCGGCACTTGGAGGGCTCCTTCATGTTTTCCTTTTGTTTTTAGTAAGTAGCTAATAAAGCATTGTTATTGCAGACTTTGGTAAGTCTTAAGTGTATATATGAGAGCAACTTCCCCAGGATTTGAAGACCTTGTATTGCATGCCTTTTACAGTACATCTTGTTTTGTTTTGTTTTCTAAAGAGGTGAGGTCTCATTGTGTTCCCTAGACTGGAGCGTGGTGGCACAATCATAGCTCACTGTAACCTTGAACTCCTGGCCTCAAGCTATCCTCCTGCCTCAGCCTCCCAAAGTGCAGGGATTGCCGGCATGAGCCACTGCGCCTGGCCCGTCTTGTTTTTTTGTTTACTCTGGTCTGAAATGTAACTTCTACTACCTAATTGATACTTGAGGCCAAACCATGTAGGCTGGGTTGCTCTAGCAATAAGTGGCTGCTTCCAGCAGGATCCCCTCATGGCTTCAGTAACCTATCACAGTTTGGGACTGTTGGTTATTGAGGGGCTGTGAACAAGTCTCCCCCTTTCTGCATGCGTGTATTGTAGGGTCCTTTTTCATGAGCTGCAAACTGGCTGCCTTTTGTCAGGCCAAATGCAGCAGTGTTTTGTTTGCTAACGTGGTTTTTAAAATCTTGAATTTGACCTTTTATCTGCATGACCCTTGCTTTACATTAGAGACAAGACTTGAGAGATTGGAGCACATCATTGCTGTCTTTATTTGTGTTAACTTCATACATTCATGTGAGGACTGCCCTTGTTCTTTTACATTTTCAG
Seq C2 exon
CACCTCTTGGACAGGATTAACGAATATGTGGGCAAAGCCGCCACTCGTTTATCCATCCTCTCGTTACTGGGTCATGTCATAAGACTGCAGCCATCTTGGAAGCATAAGCTCTCTCAAGCACCTCTTTTGCCTTCTTTACTAAAATGTCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165699-TSC1:NM_001162426:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF043887=Hamartin=FE(48.6=100),PF043887=Hamartin=PU(0.1=0.0)
A:
NA
C2:
PF043887=Hamartin=FE(14.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGTGGCCCTATGCTTGTAAA
R:
CTTGAGACATTTTAGTAAAGAAGGCA
Band lengths:
256-1717
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)