GgaINT0125144 @ galGal3
Intron Retention
Gene
ENSGALG00000003500 | TSC1
Description
NA
Coordinates
chr17:7386917-7387401:-
Coord C1 exon
chr17:7387286-7387401
Coord A exon
chr17:7387041-7387285
Coord C2 exon
chr17:7386917-7387040
Length
245 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
TGTGTATTACTTTTCAATAGGTT
3' ss Score
8.99
Exon sequences
Seq C1 exon
TTTCAGGGACGTCTACCCCATATTCCACTCCTCGGCTAACACTATCACAACTGCCAGGGCAGCTACCTCAGATTCTGAGCCCGCAGTCAATAAAGCTGTCAACTGAGCCACAGCAG
Seq A exon
GTAAAGCAGAGGATCACATGCAGTGTGTGTTCAGAGCTTTGCACTTTGTGTGTACCTTCTTGTGACAATCTCAAAAAATCATGATTCTGAGAAGTACTGTGAACTGTTCAGAGTTTTGCATACATTTCAGATTTTATTCCCATCTTGTTTGCTATGTCAGAACCTGGGTATGGATGTCTCTCAGTACACGTGTTCTTTTTAGGAGCTTTGCTGATTTGTGTTTATTGTGTATTACTTTTCAATAG
Seq C2 exon
GTTACCATCTGGAGTCCTTCTGCAGTTTGTGGTATGACCACTCCACCAACCTCCCCTGGAATTGTCCCATCAGAGTCATCCCAGTCAACATCACAACCTTACAGCAAAGCTTTTGGCACATCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003500:ENSGALT00000005537:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.846 A=NA C2=0.845
Domain overlap (PFAM):
C1:
PF043887=Hamartin=FE(5.3=100)
A:
NA
C2:
PF043887=Hamartin=FE(5.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGACGTCTACCCCATATTCCA
R:
ATGTGCCAAAAGCTTTGCTGT
Band lengths:
232-477
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]