DreINT0131053 @ danRer10
Intron Retention
Gene
ENSDARG00000077093 | scaf4a
Description
SR-related CTD-associated factor 4a [Source:ZFIN;Acc:ZDB-GENE-030131-9003]
Coordinates
chr10:25746488-25747477:-
Coord C1 exon
chr10:25747401-25747477
Coord A exon
chr10:25746673-25747400
Coord C2 exon
chr10:25746488-25746672
Length
728 bp
Sequences
Splice sites
5' ss Seq
GAGGTGTGT
5' ss Score
6.14
3' ss Seq
TGGGGATGTTGTTTTTTCAGGTC
3' ss Score
8.46
Exon sequences
Seq C1 exon
GAAAGTCTGATGAATTCAGATGCATCTGCGAGGTCTGCCCATGAAGACAAGAGGTCAAGGTCACGCTCGGGGTCGAG
Seq A exon
GTGTGTACACAAAAATCCTTATGAACAACAATAACCATTCATCTAAAGCTCACAGTTTTTATTTTGAGTCCTTGCGGCAAGGTTAGAGGGTCATGAACCAGTACAATAACATTTTAGACTTTTATTTCACTTCGCCTGCCTTAAAGAGATAATTCACCCCAAAAGATCAATTCTTTCATAATTTAATCACCTTTTACTTGTTCAAATATACAGAATTTTTTTCCTACTATGGAGATCGATGGGTCCCAGCAATACTTTCTTTTGTGTTCCAACAGTAGAAAGAAACTCATAAAGGTTTAAAACCACATGAGAGAGAGTAAATGATAACATAATTTTTCTTTTAGGTGAACTCTCTCTTTAAAAGCATGTTGGTTTCCTGCAAATATATGCTGCAATTGACCATTAAACACAACAAAACGTACTTCTATTCCACACACCTTCGTAAGCTCCCTGTATTTTACACAACACACATGCCCCTTGTCTGCTATGTTTAATTAACAAATAAATGCACACTCGTGTGTATTTTAACTCTGCATGAAAAAAAAAATAGTCTTTTTTTGCAAGGATAAACCAGAAGAATGGCTCATCAAGATGATATGAAATATTTAAATTTCTTCTGCAATTGTAAATCATTGTAATTGTATATCATTGTATTCTGTGATTTGTTACAAAAACATGAAATCCTAGAAAAATATAGTAAATTGTAAATGGGGATGTTGTTTTTTCAG
Seq C2 exon
GTCTCCTAAAAGAAGAAGGTCTCGATCCAATTCCCGGTCCAGACGAATGAGGCATCGACGATCTCGGTCTCGAGAACGGCGGCGTCAGTCACCTCGCTCGCGCTCTCAGGAAAGGAGAGACAGAGAAAAGGAAAGAGAACGAAGACAGAAAGGCCTCCCTCCTGTTAAAAATAACACACTCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000077093:ENSDART00000140483:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.921
Domain overlap (PFAM):
C1:
NO
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:
CAGATGCATCTGCGAGGTCTG
R:
CACTGAGTGTGTTATTTTTAACAGGA
Band lengths:
246-974
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]