GgaINT0125142 @ galGal3
Intron Retention
Gene
ENSGALG00000003500 | TSC1
Description
NA
Coordinates
chr17:7387853-7389555:-
Coord C1 exon
chr17:7389482-7389555
Coord A exon
chr17:7388032-7389481
Coord C2 exon
chr17:7387853-7388031
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
GTACATACGTTCTCTCTGCTATTAGGAAAGGCTGCAAACTAGCAGTTTTTACTTGACTTATTTCAGAAGGCTTACAGCAAAACCTTTTCTCTTGACAACAGTGTGTGCCAGTGGTGTTTTGCCATCCATTTTTCCTAAGTCCACCAGGTAAATGTAAAATTTCTTCATCCAGGCTCACAGCTGGATGAATAAGCAGCCTTTTGTCGTGAAGGGCCATTAACAGTGACGATGGGGCTCTGTATTCATTTTGTATCTGGGAAAGAATCTGGCTCTTACCCAACTGTTGACTTTGTCTTAACTTTATGGCTTAATAGTCAAACATTCTCAAAGTTCTAAAAAAAAAATAATAATAAAAAAAAATTCCTTATAATAGGAAGGAAACATTGGCGTAAGGTTTGGGTCATATTTTTTGGTTTGTTGAAGTACTTGGTGGGATTTGCCTGTTTGAAATGGCTTTGGTGTGTCTTTTGTTTTGGTACTTAGACATTGGTTCCATTAACAGATCAGTTCTTTTAACAGGTATGTCTTAACGTCAGCTGTATTAGTTTTCTTTAGAAATAGGCTCATTTGCCTGCAGCAGCACCACTTGCTGCTTTTCTCTTGTCTCCACAGGCCCAGCCACTGAAGAGGAGAAATTGACTCTTGTTGCTGCACAGTAGTGCTCTTGCCCTGCTTTTCAGAGCCACTAGGAAAACACTGCTAAATGGGAACCTATTGAATATCACAGTGCTCAGTTTTGCAGGCTTCTCTCAGACAGGGAGGAGGGGGATGGAGAGAGGGTGGCACCACTGAGGAATTCAGTTGGCACAAAACTACAATTTGAAGCCTTCTGATTTGGTATCTTTCACATGTATTTATATTCAAAAGTAACTCAGCCTTTAATAGACAGCCTTCTGTGCTTTCTCTTCTTTACAGTGAACTTCCATCCCCTGAAATATTGGGCAGACCTAATATGGCTGCTAAATTTAGTGAGAAAAGATTTCCAAGTGAAGGTGGTAGTAATGATAAAGGACATTCCCAAAACTTAGGAGTCAAAACACAGACCTGAAACTGGCATTGCAGGTGGCAGTTGCTTAAATAATATGGTTCCCTGACTGCTGGCATTTCTAAATTTTGGCAACCGACATCTGTGTCTAAATGAGCTGATTTCTACAGCTGCTGAAGCTCGGGATCAACCGAATCTTCATATGCTATTCCTCCTTTCCAGAGTGCTCCATGGCAGACCTTTATGGATCTCTATGTCAAAGCTATTTGTCTCCTATCCGAGACCCCCTTTTACAAGTCATCTGGTTGCAATTTCTGTACGGTGCCTTGTTCTGCATTTGGGAGCATACAAGGCTGTCTGGATCAAATGAGCCATCCTACAAGCCAATTCCTGATATCTCCAGGAACCTTTGTTCGTAGCAATAATTGACTAACTTACTCTTTTGGATCCAAAAACTGTCTGCAG
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(5.2=100),PF109733=DUF2799=PU(1.7=4.0)
A:
NA
C2:
PF043887=Hamartin=FE(13.1=100),PF109733=DUF2799=PD(96.6=91.8)
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:
TGGAACATGTGCGAATTCATCCA
R:
CATAGCTGCTCTGTGTGTCAA
Band lengths:
246-1696
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]