DreINT0154637 @ danRer10
Intron Retention
Gene
ENSDARG00000088347 | sp1
Description
sp1 transcription factor [Source:ZFIN;Acc:ZDB-GENE-030131-2829]
Coordinates
chr11:27250-28224:-
Coord C1 exon
chr11:27840-28224
Coord A exon
chr11:27321-27839
Coord C2 exon
chr11:27250-27320
Length
519 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGT
5' ss Score
10.49
3' ss Seq
TGTGTGTGTGTGTGTGTCAGATC
3' ss Score
10.37
Exon sequences
Seq C1 exon
AAAACACCCTGCTGGAGAACCTGCTGATCCAGAGGGAGAGGAGGCACTAAGGACACTCTCACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACTCGGGCCGCAGCTGGGCTCTCAGTATCTCAGACTCGCACACTGGATGATAAGAAAGTATTCTGAACGGCCAAATGTCAAGAGTAGAACCGAAGAAGCCCATTGGCTGCGGCCACAGCGACTCGTCTTCTGATTGGCTCGTCGCTCCGCCGCTTTGACTCTGGCCTTTCTGTTCATCAAGTTCGGTTGAGTTGTTTGAGAGTTCATGTCAGACTTGAAGAAGCGTGAAAAACTCGCGCCCTCGCACAGAATGAGCG
Seq A exon
GTGAGTAGCGCTGAAATCCGCTTATGAACGCCGCAGAGTGCCATCTGTAACCGGCGCGAGACTCTGCGGGCAGTGTGTGTCTGTGTGTGTGTGTGTTGTTGAACTGATTCGCCGAAAACACTGAGCCGTGTTGTTCCTGAGCCGCTGAGTGATCAGGAGTGTTTATAAGCGCTCCATCGCGGACTCTGAGCTGATTTTCCTCAAGTGAGCTAAAGTTAGCCGAGATCTCCAGCGTTAGCGTTAGTTGAAGTGATCTTTACAGCGACCTACATTGAGTTATATAAGAGTGGTAAACAGGAGTGTGTGTGATGTGATCATGTATGCGACGGAACTCACGCACACACACACTCGGGGGTTTTGGCTAATATTGGTGTTTTGATGAGCTACAGGGCTAAAGCTGATGTGTGAGAGTGAATATGGCGCGTGTTCGGCTAACTCTGCTAACTGTCTCGCGCACTACATAGTGATGTTGTCTGTGCCCTGATCAGTGTGCACTGTGTGTGTGTGTGTGTGTGTCAG
Seq C2 exon
ATCCACAGAAGAGCTCCATGGCGGACTCAGAGCCCGGCTTCCCCCAGAAGAGCAGCTCCAGCTCGGCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000088347:ENSDART00000124104:1
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=0.978
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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:
ACACACACACACACACACACA
R:
CGCCATGGAGCTCTTCTGTG
Band lengths:
342-861
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]