MmuINT0159246 @ mm9
Intron Retention
Gene
ENSMUSG00000038482 | Tfdp1
Description
transcription factor Dp 1 [Source:MGI Symbol;Acc:MGI:101934]
Coordinates
chr8:13370481-13371022:+
Coord C1 exon
chr8:13370481-13370646
Coord A exon
chr8:13370647-13370878
Coord C2 exon
chr8:13370879-13371022
Length
232 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
GCTGTTGCTCTGTCGTCTAGGCT
3' ss Score
6.48
Exon sequences
Seq C1 exon
GAAGCGGAACAGGAAGGGCGAGAAGAATGGCAAGGGCCTGCGGCATTTCTCCATGAAGGTGTGTGAGAAGGTGCAGAGGAAAGGAACCACCTCCTACAATGAGGTGGCTGACGAGCTGGTGGCAGAGTTCAGCGCTGCCGACAACCACATTCTACCAAACGAATCA
Seq A exon
GTAAGTGTTCTGGCAAGACATGGGGCTTGACTTGCAGCCACTCAGTATAGCGTGGTTCAGCCTGTCAAGCTGAGGCAGTGATGGGGGCTAGGAAACCCTCAGGTTTAAGGCATGAAGCAGGACAGAGTGGGTGGGCCAGGAAAATCCCCTCGGGACATGCTCGTGGTATGAACCTCAGGTGTGAATTTCCAAGCCATTGGATCACCAAGGAGGCTGTTGCTCTGTCGTCTAG
Seq C2 exon
GCTTATGACCAGAAGAACATCCGGCGGCGTGTCTACGATGCCTTAAATGTGCTAATGGCCATGAACATCATCTCCAAGGAGAAGAAGGAGATCAAATGGATCGGCCTGCCCACCAACTCAGCTCAGGAGTGCCAGAACTTAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038482-Tfdp1:NM_009361:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.291 A=NA C2=0.073
Domain overlap (PFAM):
C1:
PF0231915=E2F_TDP=PU(56.6=83.9)
A:
NA
C2:
PF0231915=E2F_TDP=PD(41.0=70.8),PF087815=DP=PU(4.1=12.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGAAGGGCGAGAAGAATGG
R:
TTCTGGCACTCCTGAGCTGAG
Band lengths:
294-526
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: