DmeINT0015180 @ dm6
Intron Retention
Gene
FBgn0038244 | CG7987
Description
This gene is referred to in FlyBase by the symbol DmelCG7987 (FBgn0038244). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (1 unique). Gene sequence location is 3R:14570472..14575887. Its molecular function is described by: DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding; DNA-binding transcription repressor activity, RNA polymerase II-specific; sequence-specific DNA binding; RNA polymerase II regulatory region sequence-specific DNA binding. It is involved in the biological process described with: negative regulation of transcription by RNA polymerase II; regulation of transcription by RNA polymerase II. 12 alleles are reported. The phenotypes of these alleles manifest in: sarcomere; myofibril; Z disc; wing. The phenotypic classes of alleles include: viable; flightless; visible. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed within 00-06 hour embryonic stages.
Coordinates
chr3R:14574548-14575887:-
Coord C1 exon
chr3R:14575771-14575887
Coord A exon
chr3R:14574886-14575770
Coord C2 exon
chr3R:14574548-14574885
Length
885 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
GAGAACTGCATATTTTGCAGGGC
3' ss Score
5.63
Exon sequences
Seq C1 exon
ACGCAATGGCAATTCCTCTTTCTCCGGTCGTTCGTGAACATTTTGCGAGAAAACTTTTCGCCGCATTTAAAAACGTTAAAGACGAAGCATGCGAACGGCATAAACACTGGATTTAAG
Seq A exon
GTAAAACAACGCAGCAACAGTACTTAGTGGACGGTAGACCTATTTAACCTCAAAATGACACCGACAAACTCGGCTGAAAATTAAAAATAAAATATTCCAAAGTATCGGCTGTGCAAGAATTTTGGGCGTGTGATGTGTGATGTAATAGCGTGGCCGCAATGGCTGTTACCGTCTGTGGCTTTTTTTCATATAAATTAATTGGCCAGCTCTTTGTTTACGTTTACGCCAAGCTTGCGGTCTGGAATATAAATAAAAACGCCGACTTAACCTCATTTATGGTCCAAATTGGTGTTTATAAGTTGGAATATTTTGCATGTAAAAAAGCTTAGACACGAACATTGCTGTCAGGATAGGCGAGTGCCGTGAGTGGAAGCGAGATGACTAGTGTGTGCGGCGGTTGGAAATCAGTGGTGTGCAAATTTTCAAGAACGAAAATGCTAGATTCAAAATATTTTATTTTATGTGCTAACACTTAACATGTCATTAAAATTGTTAGCAGTCTCAGATACATCCGTTTAATTTGAATAATTTTCTTTTTTTAAAGATACAAAAGAATAGTTATTTCCAACAATTCAATATACAAAATTTAATCTAAGTCAAAACTATGTACTATGTGTAATATTAATACAAGCATTCTTCTGACCAGTAGTTCAGTTAATTTGTATTTTGCAATTCATTATATTTTATTATCTAGCTATTTTTTTTTTAAAGTAACTATTGAATGTCATCGACCAAAGATCTGGCAACGCCGTAGTCGCTCTCCCTCTCCCACCGTCTTCGGCCTTTTTGAGCACATGTGCCACCGATTGTTGCTCGCAACGGATATTTTTGTGCCTCCCGTTTGTTTATGTGTGCAACGAAGTGAGAGAACTGCATATTTTGCAG
Seq C2 exon
GGCTAGCGAGTGATGAACAACCAGCGATATGGCGGCATCCAGTGGATACAGCACCACGTTTCCGCGGGCGACTCCTCCGAGGTGGACATCCTGGAGTCGGATGGTGGAGCAGGGGCCTCGGGTGAGGATCTGGACCATGTGGCGGCCGAGAATCTTATATTCATGGCCCGCGACGGTCAGCTAAGTGAGATAATGGCTGCCAACGAAGCTGGTAGAACGGTCCTGGTCACCGCCGACGGCACCACGGTGGCCTATGCGGAATCCTTCGACGATGACGCCCAGGTGGTCACCGAGGAGGTAATCACAGACGACTGGGTGCAGCACCAAGGCGCCGAGCG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0038244:FBtr0082978:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.165
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
FBpp0082438
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0082437
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:
TTGCGAGAAAACTTTTCGCCG
R:
CGTCGAAGGATTCCGCATAGG
Band lengths:
346-1231
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)