GgaINT0125142 @ galGal4
Intron Retention
Gene
ENSGALG00000003500 | TSC1
Description
tuberous sclerosis 1 [Source:HGNC Symbol;Acc:HGNC:12362]
Coordinates
chr17:6735119-6736821:-
Coord C1 exon
chr17:6736748-6736821
Coord A exon
chr17:6735298-6736747
Coord C2 exon
chr17:6735119-6735297
Length
1450 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAT
5' ss Score
7.87
3' ss Seq
GATCCAAAAACTGTCTGCAGGTG
3' ss Score
5.35
Exon sequences
Seq C1 exon
CCAATGATGGAACATGTGCGAATTCATCCAGAATTAGTGACTGGATCTAAGGACCATGAACTGGACCCACGAAG
Seq A exon
GTACATACGTTCTCTCTGCTATTAGGAAAGGCTGCAAACTAGCAGTTTTTACTTGACTTATTTCAGAAGGCTTACAGCAAAACCTTTTCTCTTGACAACAGTGTGTGCCAGTGGTGTTTTGCCATCCATTTTTCCTAAGTCCACCAGGTAAATGTAAAATTTCTTCATCCAGGCTCACAGCTGGATGAATAAGCAGCCTTTTGTCGTGAAGGGCCATTAACAGTGACGATGGGGCTCTGTATTCATTTTGTATCTGGGAAAGAATCTGGCTCTTACCCAACTGTTGACTTTGTCTTAACTTTATGGCTTAATAGTCAAACATTCTCAAAGTTCTAAAAAAAAAATAATAATAAAAAAAAATTCCTTATAATAGGAAGGAAACATTGGCGTAAGGTTTGGGTCATATTTTTTGGTTTGTTGAAGTACTTGGTGGGATTTGCCTGTTTGAAATGGCTTTGGTGTGTCTTTTGTTTTGGTACTTAGACATTGGTTCCATTAACAGATCAGTTCTTTTAACAGGTATGTCTTAACGTCAGCTGTATTAGTTTTCTTTAGAAATAGGCTCATTTGCCTGCAGCAGCACCACTTGCTGCTTTTCTCTTGTCTCCACAGGCCCAGCCACTGAAGAGGAGAAATTGACTCTTGTTGCTGCACAGTAGTGCTCTTGCCCTGCTTTTCAGAGCCACTAGGAAAACACTGCTAAATGGGAACCTATTGAATATCACAGTGCTCAGTTTTGCAGGCTTCTCTCAGACAGGGAGGAGGGGGATGGAGAGAGGGTGGCACCACTGAGGAATTCAGTTGGCACAAAACTACAATTTGAAGCCTTCTGATTTGGTATCTTTCACATGTATTTATATTCAAAAGTAACTCAACCTTTAATAGACAGCCTTCTGTGCTTTCTCTTCTTTACAGTGAACTTCCATCCCCTGAAATATTGGGCAGATCTAATATGGCTGCTAAATTTAGTGAGAAAAGATTTTCAAGTGAAGGTGGTAGTAATGATAAAGGACATTCCCAAAACTTAGGAGTCAAAACACAGACCTGAAACTGGCATTGCAGGTGGCAGTTGCTTAAATAATATGGTTCCCTGACTGCTGGCATTTCTAAATTTTGGCAACCGACATCTGTGTCTAAATGAGCTGATTTCTACAGCTGCTGAAGCTCGGGATCAACCGAATCTTCATATGCTATTCCTCCTTTCCTGAGTGCTCCATGGCAGACCTTTATGGATCTCTATGTCAAAGCTATTTGTCTCCTATCCGAGACCCCCTTTTACAAGTCATCTGGTTGCAATTTCTGTACGGTGCCTTGTTCTGCATTTGGGAGCATACAAGGCTGTCTGGATCAAATGAGCCATCCTACAAGCCAATTCCTGATATCTCCAGGAACCTTTGTTTGTAGCAATAATTGACTAACTTACTCTTTTGGATCCAAAAACTGTCTGCAG
Seq C2 exon
GTGGAAAAGACTAGAAACTCATGATGTTGTGATAGAATGTGCCAAAATCTCCCTGGACCCTGCAGAAGCCTCATATGAAGATGGCTATTACTCTGCGTCTCGGAAATCCTGTACAAACTTAAAACATCATCAAACTGACCCCAGTGCCAGCCATTACATTGACACACAGAGCAGCTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003500:ENSGALT00000005537:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.227 A=NA C2=0.328
Domain overlap (PFAM):
C1:
PF043887=Hamartin=FE(3.3=100)
A:
NA
C2:
PF043887=Hamartin=FE(13.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAACATGTGCGAATTCATCCA
R:
CATAGCTGCTCTGTGTGTCAA
Band lengths:
246-1696
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]