DreINT0130925 @ danRer10
Intron Retention
Gene
ENSDARG00000062968 | sbf1
Description
SET binding factor 1 [Source:ZFIN;Acc:ZDB-GENE-040718-139]
Coordinates
chr4:9961682-9963367:+
Coord C1 exon
chr4:9961682-9961780
Coord A exon
chr4:9961781-9963141
Coord C2 exon
chr4:9963142-9963367
Length
1361 bp
Sequences
Splice sites
5' ss Seq
AATGTATGT
5' ss Score
5.87
3' ss Seq
TATTTGTTTCTTCCCCTCAGGAG
3' ss Score
10.26
Exon sequences
Seq C1 exon
CTCATAGCCAATCAGGTGGAGCGCATTCGAAAGGAGACTGGAGATCCTCATAAAGTCATGAAGCACATTAAGGAGCTGGCGGAGCAGCTTTTCAAAAAT
Seq A exon
GTATGTCCGATTTGTGGGTCTTATATGAATATATATTTTTGTCCAGTTTTTTTTCACAACCTTTTATTTTTAAGCTAACTGTATATATACATACAGTTGAAGTCAGACTTATTGCCCCCCTGTTTATTTTCCCCCCAATTTCTGTTTAACGGAAAGAAGAATTTTTCAAAATATTTCTAAACATTTAATAACTCATTTCTAATAACTGATTTATTTTATCTTTGCCATGATGACAGTAAATAATATTTGACTAGATATTTTTCAAGACACTTCTATACAGCTTAACGTGTCACTTAAAGGATTAACTAGGTTGACTAGGCTGGTCAGGGTAATTATCGTATAACAATGGTTTGTTCTGTAGACTATTGAAAAAAGTATATAGCTTAAAGGGGCTAATAATTTTTACCTTAAAATGGTTTTTAAAAAATTTAAAACTGCTTTTATTCTAGCTGAAATAAAACAAATAAGACTTTCTCCAGAAGGAAAAATATTATCAGACATACTGTGAAAAATTCCCTGCTCTGTTAAACATCATTTGGGAAATATTTTAAAAAGAAAAAAATAATTCAAAGGGGGGCTCATAATTCAATTGTACGTTTTGATTTTAAATTTTATCAATAGTTTTGTCATTTACCTCACACTAAAAAGGAGAAAAATTCCAGTATTTCCAATATTTATCATTTGAATAGATAAACAGTGCGTTACATTTTTAGCATTACAAGTTTTGAAATGCTAATTTATTAGTAATAATAGTTGTTTTAGATAAATTATGATTTTGCATATGAACATTACAATAATGTTGTGATGTCTCAATCAGATTTCAACACAATTATAGTTAATTTTGTAGTTTATTTAAATTTTTATTACAATATACAATTTTAATATTCGTATTATTTTAAATATATAATTCCCACGCTTCTTGAAAAAAGTACTTCATAGTGCCTGGATTTCAGACAGACCAATTCAAGACCTCGAAGAGGTTTAAAAACATACCTAGGTTCTTGAAAATGCTTGAATTTGTAGTTTATGGTGTTATTTCAACAATTATGCTGTTTTGCTTTAAAAAAAAAAAAAAAACTGAATGAAAAAACTGAGAAATTCTTAATTTAAAACCTTAAATTTAATATTTTATACTAGAACTGTGACAAATAATGCACATTTGAACAACATATCACAAACCGCATTTGAATATTACCAGTGTTGAATGAACTGGAAACTGATGGTGTTTTAAGAAGTCCTTGGATCTGCTGTTCATAAAAGAGTGAAGACACATGAAATATAGCTATTGACTCCATTTTTAATAATACTTTTGAAGATTATTTGTTCCCTCTAAAAACAATCTATTTGTTTCTTCCCCTCAG
Seq C2 exon
GAGAACCCGTACCCTGCAGTGACCATGCACAGAGTCCAAAGGACAGCTGAAAGCGCACATCCTCGGCTGCCACAGACCTCTTTTCCCCTGCTGGATGAGGTGGCCGTGCAGCTCTTCATAGACCACGCTACAGCTAAGCTCAAAACTGCCCCGCCGGTGGTCAAAGCCGAACTCAAGAGCATGGTTCCAACCGGACCGCCGCTCGGTGAGACAAAGTTCACTTACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062968:ENSDART00000109452:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.061 A=NA C2=0.220
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF123353=SBF2=PU(3.2=9.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCATAGCCAATCAGGTGGAGC
R:
TGAACTTTGTCTCACCGAGCG
Band lengths:
318-1679
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]