DreINT0130935 @ danRer10
Intron Retention
Gene
ENSDARG00000062968 | sbf1
Description
SET binding factor 1 [Source:ZFIN;Acc:ZDB-GENE-040718-139]
Coordinates
chr4:9978799-9979565:+
Coord C1 exon
chr4:9978799-9978991
Coord A exon
chr4:9978992-9979437
Coord C2 exon
chr4:9979438-9979565
Length
446 bp
Sequences
Splice sites
5' ss Seq
TTGGTATGC
5' ss Score
5.91
3' ss Seq
TGTATGTTTGTATTATTCAGTTG
3' ss Score
6.44
Exon sequences
Seq C1 exon
CCTAAGCTTCTGAGGCCAACTCTGCTGCCTGGTGAGGAGTTTGTTATGGACGGGATGCGGGTGCACCTTATCACAGATGGTCGAGAGGAGGCCACGGGCAGTATGGGAGGACCACCGCTGCTCCCTGCTGAGGGGGCAATCTTTCTCACTTCTTATAGGCTCATCTTCAAGGGCACTCCCACAGATCCGCTTG
Seq A exon
GTATGCTCCAATTGGCCGAGAACTGTGCTCATTTGCATAATTTACTTGTTAAAACCTATTGTTTCCATAGTTCAAGCTTCTACTCATTTAAATTTATAAAATACTTTTTCAATAGTCATTTAGTTTGAGTTTAAATTTAGTCTTTAGCATTAAAGTTTTACTTACAGTATGTGGACTTACACAATTCACAGTATTAACAAACTATTAACTAACACTACTAGCTTAATAAACTACTAATTTACTGTTCATTAATAGTTAGTAAGGATAATGTTGGGTTTAGGTTTTGGGTAGAATTAAGAATGCGGAATAAGATTTATAACTAGTAATAAACAGTTAATGTCTTAATAATTGGCAGGTAATAAGCCAGTAGTTAATAGCATGAGTTGTATTGTTTATTTTCGAGATTTAGGATGCTCACTTAACTCTTGTATGTTTGTATTATTCAG
Seq C2 exon
TTGGAGAGCAGGTGGTCACTCGCTCCTTCCCTGTCGCCTCCCTCACGAAAGAGAAGCGGATTTCTGTTAGTCTTCCCATGGATCAGTTCATCCAAGAGGGTCTCCAGTTGCGATCCTGCACTTTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062968:ENSDART00000109452:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.185 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0289315=GRAM=PU(74.4=98.5)
A:
NA
C2:
PF0289315=GRAM=PD(24.4=48.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGCTTCTGAGGCCAACTCTG
R:
CTGAAAAGTGCAGGATCGCAAC
Band lengths:
318-764
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]