DmeINT0027569 @ dm6
Intron Retention
Gene
FBgn0020378 | Sp1
Description
The gene Sp1 is referred to in FlyBase by the symbol DmelSp1 (CG1343, FBgn0020378). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (4 unique). Gene sequence location is X:9729648..9756369. Its molecular function is described by: sequence-specific DNA binding; transcription regulatory region sequence-specific DNA binding; DNA-binding transcription factor activity, RNA polymerase II-specific; DNA-binding transcription factor activity. It is involved in the biological process described with: positive regulation of transcription by RNA polymerase II; regulation of transcription, DNA-templated; imaginal disc-derived leg morphogenesis. 16 alleles are reported. The phenotypes of these alleles manifest in: cell cluster organ; portion of tissue; anlage; first segment of antenna; presumptive tarsal segment 4. The phenotypic classes of alleles include: visible; viable; size defective; lethal; homeotic; cell shape defective. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of extremely low expression. Peak expression observed within 06-18 hour embryonic stages, during late larval stages, at stages throughout the pupal period.
Coordinates
chrX:9729648-9730677:+
Coord C1 exon
chrX:9729648-9729870
Coord A exon
chrX:9729871-9730299
Coord C2 exon
chrX:9730300-9730677
Length
429 bp
Sequences
Splice sites
5' ss Seq
ACTGTGTGC
5' ss Score
-1.29
3' ss Seq
TTTTTCCCTTACTCTCCAAGATC
3' ss Score
6.76
Exon sequences
Seq C1 exon
AACAGTTGCAAGCCTTTGAACGATCAGCGACGACGGCGTTACTTTTGGCGCGGATACAGCAGCGACACTTTTTTTTCGTTGGCAGGCGCCTCCTGTCACCAAACAAACAAATAAATAAACAAATAAACATAAAAACAAACAAGCAAATAAATAAACAATAAACCAACAAGCAAACAAACAAACATAAACAAGCCAACAAGCAGCCAAGCTAAACAAAACAACT
Seq A exon
GTGTGCATTTTTGGTTCGAGTTTCCTTTAATTTCCATCGCTTATATTTCATTTTTTTTTTGCCTGTGTTCCTTAGAAAAGAAGTCTATAAAGAATAAAAAAAATAAAAAAAAAATTAAGCCCATATATAGGCACAAAATCCCAGTGACAATAAGAGCAGTCAAACATTGCAACTCTCAGCAGCAAACATCAGCCGACGGCCGAGTGAAGAAAAGTGCAACGCCGACGGACTCGAGAAAAGATACAGATACAGATACGGATTATACATATCTGGGCTATTAGCTGGGCCATAATCTGCTCTCAAGCGATTTAGCCCACTTTGCTTTTTTTCTGAGTGCGTGTGTGCTTGTGCTGTGCTGTGCTGTGCTGTGCTGTGCTTGCCAATCCATTTGTCCATGTCCTTTACATCTTTTTTCCCTTACTCTCCAAG
Seq C2 exon
ATCAGTGAGCCTGGCCTGCAACAATAGTCGCAACAAAGAAAAAAGTAGTTGAGTTGAGCAAGAAGAAAAGAATAGAAAATCGAACCCTAAACCCAAGTGGCCGCAAAACAAAGCAGAAGCAAAACAGACAGCATCATTGTGCGCCTCAAATTGACATCAGCAGCAGCAGCAGCAGCCGCAGCAGCAACGACAACTGCCACTGCCACTGCAGCAGCAGCAACATCAGCAGCAGCAGGAGACGCAGCAGGAACATCCACAGCAACCATGTTAACGGACATGACACCGACCGCCGGTCAGCTCTACGGATCCCAGATTCCGGCCATGGGCATGAACATCAGCAATATCGCCACACACTTGCAGAAGCCACAAGTTAATCCG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0020378:FBtr0071381:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.789 A=NA C2=0.789
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
FBpp0303753
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
FBpp0271862
Other Skipping Isoforms:
FBpp0301973
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACTTTTGGCGCGGATACAGC
R:
GCTGATGTCAATTTGAGGCGC
Band lengths:
345-774
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Neural diversity
- Neurogenesis
- Neuronal activity
- Splicing factor regulation (brain)
- Splicing factor regulation (SL2)