DreINT0131065 @ danRer10
Intron Retention
Gene
ENSDARG00000077093 | scaf4a
Description
SR-related CTD-associated factor 4a [Source:ZFIN;Acc:ZDB-GENE-030131-9003]
Coordinates
chr10:25749449-25750763:-
Coord C1 exon
chr10:25750634-25750763
Coord A exon
chr10:25749592-25750633
Coord C2 exon
chr10:25749449-25749591
Length
1042 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TTGTCAATGTGCTTCTGCAGCTT
3' ss Score
7.76
Exon sequences
Seq C1 exon
AGTAAGATAGTACGAGTGCTCAACCTGTGGCAGAAGAATGGAGTGTTTAAGATCGAGGTCATTCAGCCTCTGTTGGACATGGCTGCTGGGTCCAGCAGCTCCTCAGGCTTGGACAATGGCCCAGATGCAG
Seq A exon
GTAAGATACAGTTTTCTTTCATTTGAGATTGGTAATACAATCTACTATCATTTTTTTGTGCGAGAAATGTGAAAATATGTCTTACATTTATGAAAAATGTGTTTTTTGCAAATAATTTATCAAGGAAACTTTAAATTGACTAAAAGCAACTTTAGAAACATTGCTAAAGTAGAAAAATATAATACAATTCTAGTATTGTATTTTGTAATATAGCCCAGTATGTTGTTCAAATGAATGCTGCCTTGAGTATGAAATGCTTTTTAAAACATTTAAATAGTTATTGACCTAAAGTGTAGGTGTATTAAAGCAATAATTCACTGCAGTATGATTTTACCTCACAAATAATCATCATCATGTCTTTGTAAACTCTCAAGAATTTCATTCATCGTCTGAAGTTCTGAACACAAATGAAGATATTTTTAACCAAGTTTGAGAGATTTCATCTCTCCATTGAAGGTATATTTATGATAAACGTTTGAAGCTACAAATCATGTATAACAAGATTAAGAATAAATCAATTTAGTTTATTTCAAGTATACTGAATAAACTAAATCACTGTATGGGATGAAATAATATAATTTTGGTGGGCTTTTATTAAAAATATAGCACATTAATACATTCAGCCTGTTTTAGCATGTTTTATTTTTTGATAAAGCCAACCAGAATTGTGACTTCAATTCAAGTTTCTTGTTGATCAACCAAACATCCTTAAGCTTCAGTGGCCGAATTTGATTTAGATATGAATAGGTGCTTAATTAGATAATATTTAGATATGAATAAGAGCATCATTTTTTAAGTCAATTTTATATTTTTTCTGATTGAAGCTCTGGTTATTTAAAGTTTATTTGTATGAATTAGCTAAAACTGTCCATTTCATTGAATCAAATCAGATTTTTGATTCTGTAATTTGTGCATCAATAATCAAAACTGTTTCCAGACTACCCTGCCGAAAGTTTTCCTATAATAAAATGTTTTAGCTTGTTACATGCAATTTAAAATATCTATTAAAATATACAAGCTTATTGTCAATGTGCTTCTGCAG
Seq C2 exon
CTTCTCCACAGTCTCCCGTGAGGGAACAGGAGGCTCATCCTGTGGTGACGACAAACTCAATTGTAGCAGCTGTGCCTCAGCTTCAGAACTCGGATGCCTTTGCTGCAGTTGCTCAGCTAATTCAGTCTTCTCAAGGACAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000077093:ENSDART00000140483:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.258 A=NA C2=0.479
Domain overlap (PFAM):
C1:
PF048188=CTD_bind=PD(24.2=36.4)
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:
AAGATAGTACGAGTGCTCAACCTG
R:
CTGCTGTCCTTGAGAAGACTGA
Band lengths:
270-1312
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]