DreINT0168617 @ danRer10
Intron Retention
Gene
ENSDARG00000057918 | tsc1b
Description
tuberous sclerosis 1b [Source:ZFIN;Acc:ZDB-GENE-030131-3404]
Coordinates
chr21:17294032-17296119:+
Coord C1 exon
chr21:17294032-17294075
Coord A exon
chr21:17294076-17295952
Coord C2 exon
chr21:17295953-17296119
Length
1877 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAC
5' ss Score
7.2
3' ss Seq
TTCTTTCTTCTTGTTGACAGGTT
3' ss Score
9.27
Exon sequences
Seq C1 exon
ACTGCCCCTGCCAAGCAAGTCAGCTGACTGGACACACTTTGGAG
Seq A exon
GTAAACAACACCGCTTGTGGAAAATCAGTTCTTTCAGAGCACAGAAAAACAATGCCGTATTTCAGACAGGGACAAACATTTAAAGGTGAATTAAAGGGATAGCGATTCCAAAAATGAACTTTCATGCTCTAGTCATGAGGGTGAGCAAATGACAGAAAGATAATATTTATAAAAAATGTTGTTGATCCCCATTGAATTTCTTTGTATAGACAAAAACAATGATGCATTTATGTTCTGTAGAGAAAATTCATGGGAGTTATTAAATGATGGTCTCTTTTTTTTCCTAGTTGAAATAACATGCATCTAAAAAAGCAGTTTTGCTTTAGATATATCAGTTAAAGCTGAGGTTTTCTCACAAAATTATGCTTTATTTCATTTGAATTTAAATTAATTAAATTTAAAGGTGGTTCCCTGCGTTCACATGGGTTTCCTCCGGGTGCTTCGGATTCACCCACATTCCAAAGACATGCAGTACAGTTGAATATGGTAGGCTAAACTGTCCGTTGTGTATGAGAGTGAATAAGTGTGTATGCATGTTTTTTAGAGATGGGTTGCAGCTGGAAGGGCATCAGCTGCGTAAAACATATGCTGGATAAAGTGGCGCTTCATTCCGCTGTGTCGACCCAAGAGTAATAAAGGGAGTAAGCAGAAAAGAAAATTAATAAATGAATAAAGGTGGTTTTTAGGGGTGTAACAAGATCTCTTATGACAAGATCTCGCAAGATTAAATTGTGACAAGATTTCTCGTCAAGTTGAAAAGTTGTTTCGTAAGTTGTGATGTTATGATGGAGTGCGAGGATGAAATTAAGATTGGAGGCAGGATTGGATTTGAACTGCAAATTGCACACACCTGGCAACCTAGGCTGGCTTCGGAGTTGCACGTGTCACATGGTTGCTTGGGCGAGAAGCCAGTCAATAGAGTTTATAGCTAAATATAGTGTTTGCATGTCCTTTATGGCATGGAATAAATAAAATAGAAATAAAATACAATTCATTACATTCATTCAAAAACAATTCATGTTTTTTTCTTTTTTTTAAAAAAAAAGCACCCAAATTGTTTTGCAGTTTGTTTTACAGTATTTTTTTTTTCAGTTAAATAAAAATCTACTTTTCATTCATTCGTTCATTTTCGTTTCTGCTTAGTCCCGTTATGATTCCGGGGTCGCCACAGTGGAATAAACCGCCAACTTATCCAGCATAAGTTTTACGCAGCGGATGCCCTTCCAGCCGCAACCCATCTCTGGGAAACATCTATACACACTCATTCACACACATACACTACAGACAATATTTAGCTTTCCTAATTCACCAATAGCCCATGTATTTGGACTGTGGGGAAAACCGGAGCACCCGGAGGAAACCCACGTGAACGCAGGGAGAACATGCAAACTCCACACAGAAACGCCAACTGACCCAGCCGAGGCTTGAACCAGCGACCTTCTTGCTGTGAGGTGACAGCACTACCTACTGTAGTCGCCACTGCGTCGCCCTTTCCATTCATATATTAGCAAATATTTTGTTAATATTTAACATCATAAAAAATGTTTCATTCAAATAGGCTATTAGCAAAATATTTAGCAGTGTTTGCATGCCCTTTACTCTAAAGAATTCACTAAACTAGAAGTAAACTAACATCCATTACAAGTTGTTCAAGTGTGTCCTCACACCCTTAGTGGTTTTATATGGATAAAAGGCTTATTAAATTCAAAGAAACTGTAGTGATCACTGTAGTGAAAATAATGTAGTAGTCAACATTTTAAGTGGATCAAAACTTTTTATTTAGGTTGTTTTAAAACTATTTAACAACATTCATTTATGTCTTAGGACAAATTTTTATTTTATTTGTTGATTTAACTCTTCTTTCTTCTTGTTGACAG
Seq C2 exon
GTTCAGCTCCTCTGGATGAGTTGCACACACTGCGCAGTCAGCTTCTGCTTCTACACAACCAGCTCCTGTATGAGCGCTATAAGCGAGAGCAGCACGCCGTTCGCAACCGACGTCTGCTTAGGCGAATCATCAACGCCACTGCACTCGAGGAGCAGAATAATGCTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000057918:ENSDART00000145057:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.062 A=NA C2=0.054
Domain overlap (PFAM):
C1:
PF043887=Hamartin=FE(2.0=100)
A:
NA
C2:
PF043887=Hamartin=PD(5.0=67.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCCCCTGCCAAGCAAG
R:
GCATTATTCTGCTCCTCGAGTG
Band lengths:
206-2083
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]