DreINT0162310 @ danRer10
Intron Retention
Gene
ENSDARG00000019293 | tfdp1a
Description
transcription factor Dp-1, a [Source:ZFIN;Acc:ZDB-GENE-040426-2883]
Coordinates
chr9:35153135-35153593:+
Coord C1 exon
chr9:35153135-35153300
Coord A exon
chr9:35153301-35153446
Coord C2 exon
chr9:35153447-35153593
Length
146 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGC
5' ss Score
8.02
3' ss Seq
TTGGTTTCTGCTTTTTTCAGCAT
3' ss Score
8.37
Exon sequences
Seq C1 exon
AAAAAGGGGTAAGAAGGGGGAGAAGAATGGGAAAGGCCTCAGACATTTTTCCATGAAGGTTTGCGAGAAGGTCCAGCGGAAGGGTGTCACAACTTACAACGAGGTTGCTGATGAGCTTGTGGCCGAGTTCAGCTCTGGTGATAATCATATCTCTCCTAATGATGCG
Seq A exon
GTGAGCCTTCCCCTGCGGCCAGACATTGATTCAGAGCATTTCTCGTTGAGTGCAGAAGTGAAGCTTTTAAAACCAATTAAAGACTTGCTTCTTAACATATATAACATGATAAATAAACCAACGCTTTTGGTTTCTGCTTTTTTCAG
Seq C2 exon
CATGTGTATGACCAGAAGAACATTCGACGGCGTGTGTACGATGCTCTCAATGTGCTGATGGCCATGAACATAATTTCCAAAGAGAAAAAGGAGATCAAATGGATTGGTCTGCCCACAAACTCTGCTCAGGAGTGCCAGAACCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000019293:ENSDART00000077800:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.114
Domain overlap (PFAM):
C1:
PF0231915=E2F_TDP=PU(56.0=83.9)
A:
NA
C2:
PF0231915=E2F_TDP=PD(41.7=71.4),PF087815=DP=PU(20.0=12.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGGTTTGCGAGAAGGTCCAG
R:
GGCACTCCTGAGCAGAGTTTG
Band lengths:
247-393
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]