DreINT0154649 @ danRer10
Intron Retention
Gene
ENSDARG00000001549 | sp3a
Description
sp3a transcription factor [Source:ZFIN;Acc:ZDB-GENE-070410-111]
Coordinates
chr9:2756378-2756961:+
Coord C1 exon
chr9:2756378-2756712
Coord A exon
chr9:2756713-2756850
Coord C2 exon
chr9:2756851-2756961
Length
138 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
TTAAACCCGCCCATCTGCAGGAC
3' ss Score
8.19
Exon sequences
Seq C1 exon
AGGAAAGAGCTCACGTAATGACCGGTACGTAGCATCTGTGGAGCGCACACAACGATCGCTTTGAATCTTTGTGCAGGCTATGTTTGTGCTAAGCTAGGCTAACGTTAGCAGGCGGGTGAATCTGAGAGAGTTTTAGCAAATAAATACGGAGCTAAATCTATCTATAAGCCGCCGAAACGCTTGTGTGGCACCCGATGAAACACCCGCGTGCTGCAGTCACTCTCTAATGCTTGTTTTAGCATTGTTGTGTGTGTGTTTAAGCGCCTGAAGGGCCAGTGAAAGCGGGAGTCATGGCGGACAGCAGCAGCGCTCAGGACGGCGGCGGCGCGGAGCAG
Seq A exon
GTAAAAATCGCATCAAATCCTCTCCTCTCTTATTCTCTAATGCATGTGCTTTAGTGAAGTTTTCACTTTGTTCTGTTAAAACACTGGTACTTCCTGTGTGGCCACCCCCTTTCATGTATTAAACCCGCCCATCTGCAG
Seq C2 exon
GACGGACAGCCCTCGCCGCTCGCCCTGCTCGCCGCCACTTGCACCGGCCTCGGTTCGCCCGCCCCCGGAGCAGAGAACGGGGCCAGCTCTAATAACGCTTCAGCTGGGGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000001549:ENSDART00000001795:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.982
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
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:
CTTGTGTGGCACCCGATGAAA
R:
TATTAGAGCTGGCCCCGTTCT
Band lengths:
250-388
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]