DreINT0168610 @ danRer10
Intron Retention
Gene
ENSDARG00000026048 | tsc1a
Description
tuberous sclerosis 1a [Source:ZFIN;Acc:ZDB-GENE-030131-9111]
Coordinates
chr5:29058306-29060238:+
Coord C1 exon
chr5:29058306-29058418
Coord A exon
chr5:29058419-29060075
Coord C2 exon
chr5:29060076-29060238
Length
1657 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
ATAAATGTGTCCCTCCGCAGAGT
3' ss Score
10.08
Exon sequences
Seq C1 exon
AAATCTCATCAGTCACACCAATAGGTGCTATTTGTCAGTCTCTCTCTAAATCACAACCTTATCTCACTGTAACCCAAGACTCAGGTTCCAGCGCACAGACCCTCAACAATCAA
Seq A exon
GTAAGTGTCCTCCAAATAAATTATCCATTTTGTTTCAAAACAAATACAAGGCTATCTAATGTAGACATAGGCTGGTATAAGATTCTGACAGTATGATAACCTTGGTTAAAAAGATCACGGTTTCACGGTATTGTGGTTACTGCTCTAAAATATAATATTTTAAAATGTTTTTTCCCCATTTGAGCAGAAAATATTATTATTTTTTTTAAACTTTTGTTTTTTATTTGTTTTAACATAACGGAACAAACAGATCACCAGAGGCATCACATACAATTATTACATTCTTCTTATACAGTCGTATTTATAGTGCAGGTTACTCTCCCATTAGCCCCCACCCTAACCCGTCAGTAAAAGGTACTGTATTATAAGCATAAACACCAACATAGTTTCCTTCAAGTCCATATGATTCAGTCTTTTACAATCTGTAATGTGCAGTCCAAACAAAATATTTTACATATATAATATACCTATATATGTACATGTATTGAAAAAAAGTAATAATAAAAATAAAATATATAAATAAATATAAATAAGGGGAGGAGGGGGGTTCGCACTCATTGCAAATTATTTCCTAGCAAATTATATGTTTTCTATATTCTTATATATAAACCATTTTGACCAATTTTTATAGCATTTATCCATGTTTAGTCTTAAAGAAAAGGTGAGTTTCTCCATTTCAAACATATTATCTACAATTGTTATCCACTCATCCTTTGTTGGTGGAATCTCTTCCAACCATTTCAGAAAATATTTTATTTTTAAGAAACATTTATAATATTTTGGAGCAATAAACATGTCAAGGTTAATAATCGACTTCTGCTGTCTTCGTTAGTTTCAGAAACACAGATTTCTTTACACTTTAAAACAGTATCTTTGGATATCTGGATGTTTTCTGCTGGAGATACTGTTGTTAGAATGTCTTGTAAGCATAACACAACATAGACTATAATCCAAAATTAATATTGCTGTCCCAGAGCTATGGACTATTGCATACAGATGTAGCCCGAGGGAGCTTTGTTCCACCAAAGTTTAAAGCCGATGATGTACGAAAGTCAACATTTGATGTGGATCAAAAAAATGTCCTTAGACAAGAATGGGTGTTCAAAATTTTAAGGCAACTTTGATCGATATACAAGTTCTGCTGTGGTGTTATTTGTGCTTGTACATGTTCAGTAGTGTGAAGCAATTGTTAGATGTAGCTCTTCTTTTCCGTCATCAAACAGATCTCACCCTTTTCTGTATATTCTGTGGGTGTTAGTTATGTAAAAGATAATCTATGTGAAGTCATAATATCTGAAAAAGTGGTTTAGTCCAAACAAGCTGTTGGCTGTATTTTTGAGAAATGTTTTCTCCCATTGGAGTGGACTTGGAGCTCAGTAACCTTGCAGATATTTTCTTGCATACACAGCAACATTACACACTAACTAAGGTTGAATAATTGAACAAGCATAACAGGACAGCTTTAATCTCTTTGAAAATAAGCAGTGTTAGAGTTCTGGGTAAATTGATTTTTCACAAAAGCACAGAAATCTTTCAGGTTTAGTTAAATATATTGATTAGTATTCTGAACAAAAGTCGTATGTGTTTGGAATGATATGAGAACATAATTTTGTTTTGATTTGTTAATTTAAAAAAAAATAAATGTGTCCCTCCGCAG
Seq C2 exon
AGTGATGAGGTCAAATCCTCAGGGATGAAGGAGGAGCTGTGGAGCCCTTCCTCCATATGTGGGATGAGCACCCCTCCCAGTTCTAGAGGAATGTCCCCAACCACAGTTTCTGACATCTCACTTAGTGCCTCACACCTCTCAGGACGGATCCCCAGCACCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026048:ENSDART00000035400:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.421 A=NA C2=0.964
Domain overlap (PFAM):
C1:
PF043887=Hamartin=FE(5.4=100)
A:
NA
C2:
PF043887=Hamartin=FE(7.8=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:
TCTCATCAGTCACACCAATAGG
R:
CTGGGGTGCTGGGGATCC
Band lengths:
273-1930
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]