DreINT0131056 @ danRer10
Intron Retention
Gene
ENSDARG00000077093 | scaf4a
Description
SR-related CTD-associated factor 4a [Source:ZFIN;Acc:ZDB-GENE-030131-9003]
Coordinates
chr10:25743153-25744544:-
Coord C1 exon
chr10:25744431-25744544
Coord A exon
chr10:25743310-25744430
Coord C2 exon
chr10:25743153-25743309
Length
1121 bp
Sequences
Splice sites
5' ss Seq
AAGGTATAA
5' ss Score
7.08
3' ss Seq
TCATCACTGTATTTCTCCAGATT
3' ss Score
7.77
Exon sequences
Seq C1 exon
ATGATTCCTCCACGAGGTTGTGCCTACATCGTCATGATTCATCGTCAAGATGCCTATCGAGCCCTGCAAAAACTAAGCAGAGGTCCATACAAAGTCAACCAGAAAGCCATTAAG
Seq A exon
GTATAAGATGATAACAGAAAACGAATCAATTAAAGTAAATAAAGTGAATGATAATTGTCAAATGCACATTTTTTCTTTGCTTTCCACTTTAAATTCCATTATTAAATAAAGTAGAAATTACAATAGGAAATATAAATAGAACAAACATGTAAGATACAAGTAGTGCCAGAAATGTATTAGTGCATTTCATACACTGATCAAATAAAAGACTAAAATGCAGAAACACTAATAAATAATAATAATAAAAGTATTTTAAACAGAATTTTTTTTAATTTTTGTTTTAGCAAAGATGCAATACATTTATACAGGGTTTCCACAGGGTCTCAAAATGTCTTAAATCTCAAAAGCTAATTGTAGGCCTTAAAAAGTCTTAAATCTACTGAAATGTTGTGTTGTAGGTCTTTACATCTTATTTAACAAGTCTTCATTTTTCTAAAACTTTCCTTACAGTAACTTTTTCTTAAAAGTTCTCCATTTATTTACTGCTGAGGATACTGACCTGATCTAAATTTTCTATTCTTAAATTATTGTTATTGTAGACTGAAGTAATTTACAGCTATGTTTTGGTCTATTCTTGGTAAGGGTTAAAAGGTTTGTGAATGGATATATTTGAAAATTATTTAAAAATATTTCAAACTAAATTATTACTATTATTGTATTATTAAATGTATTACATTTAAATAGTTTTTTGTTAGGGCAAGTAAAAATCTTTTCTAACTGCGATATTAGAAACATACTCCTTAGCATTTAGCTCTTTATGAGTCTAAAATTTTATTCATAATGGTCCTAAAATGTCTTAAAGGCTTAACTTTAACTTGGTGAAACCTGCAGAAACTCTGTTATAGCATTGATAGTTTTTATATTGAACTTTCAATTTATGAAAGAATCATTTAAACTTATAACGGTTTGTATAAAATATTGAGCATCATAAAATCAGGATCATAGACTGGAATGATGATACTGAAAATTCACTGTTTCATCACAGTAATAAATTATATTTTAGAACATTGAAATAATACAGAGAGTATATACAAGTTTTAATTATATTTCATATAATTATTAATTTGTAATATATTTAACATTATATTCACAGTCATATATTCATCACTGTATTTCTCCAG
Seq C2 exon
ATTGCCTGGGCTCTAAATAAGGGCATTAAGGCTGAATTCAAGCAGTATTGGGATGTGGAATTGGGTGTTACCTATGTTCCATGGTCCAAGGTAAAGATGGAGGACTTGGACGTATTCAGAGAAGGAGGGATGCTGGATTCTGACACTCTTGCGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000077093:ENSDART00000140483:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.151
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=FE(55.2=100)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCCACGAGGTTGTGCC
R:
GCGCAAGAGTGTCAGAATCCA
Band lengths:
262-1383
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]