DreINT0168609 @ danRer10
Intron Retention
Gene
ENSDARG00000026048 | tsc1a
Description
tuberous sclerosis 1a [Source:ZFIN;Acc:ZDB-GENE-030131-9111]
Coordinates
chr5:29057683-29058418:+
Coord C1 exon
chr5:29057683-29057843
Coord A exon
chr5:29057844-29058305
Coord C2 exon
chr5:29058306-29058418
Length
462 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAAA
5' ss Score
4.79
3' ss Seq
ATGTACTGTTCTGTTAACAGAAA
3' ss Score
8.57
Exon sequences
Seq C1 exon
ATGGAAGAGATTTGAGCCACATGATATTGTGATTGAATGTGCCAAAATTTCACTGGATTCTAAAGAGGCGTCATCTGAAGAGGGCTACTCCTCTTTGGCGGATCACATACAGCGACGCGCTGTACACCATAGCCAATCATGTTCAGAGCTCAGTTTCCATG
Seq A exon
GTAAAATCATTTATAATGAGTGGTGTACTTTTGTTACTGTACTGTTGTCCTTCCTACTATTGAAAATAGTTGAAGGCATTTTGCTCATTTAGGGGCCGATCCCACTTAACGTGCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAGGGTGATTTTTATGACAAGACGTGTTCACAGTTTGCAACTTTTTTTTTTCTTCAATTTTTCTCCTATGTATGGCTGGTTTGTCAGACAAAATCTTGGATATCAATGGGGAGAACATAATATTGGCATTGTGATGGGTCAGATTGACCATCAAGCAAACACCTGGGTTAATTAAACACTTATTAATAGGTCTGTTTAAATCTACGTAGCAACAACTCAATTCTTGTCATAAAACTATTTAAGTTGTACATTTTTATAGGTAAATAATTGTTTTGTGTGTGTGTGAATACTGATCTTATGTACTGTTCTGTTAACAG
Seq C2 exon
AAATCTCATCAGTCACACCAATAGGTGCTATTTGTCAGTCTCTCTCTAAATCACAACCTTATCTCACTGTAACCCAAGACTCAGGTTCCAGCGCACAGACCCTCAACAATCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026048:ENSDART00000035400:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.055 A=NA C2=0.421
Domain overlap (PFAM):
C1:
PF043887=Hamartin=PD(17.5=94.5)
A:
NA
C2:
PF043887=Hamartin=FE(5.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAAGAGATTTGAGCCACATGA
R:
TGATTGTTGAGGGTCTGTGCG
Band lengths:
272-734
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]