DmeINT0012654 @ dm6
Intron Retention
Gene
FBgn0039355 | CG4730
Description
This gene is referred to in FlyBase by the symbol DmelCG4730 (FBgn0039355). It is a protein_coding_gene from Dmel. It has 4 annotated transcripts and 4 polypeptides (2 unique). Gene sequence location is 3R:25677072..25678682. Its molecular function is described by: transcription regulatory region sequence-specific DNA binding; DNA binding; DNA-binding transcription factor activity, RNA polymerase II-specific; zinc ion binding. It is involved in the biological process described with: regulation of transcription, DNA-templated. 11 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: fertile; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of very low expression. Peak expression observed within 00-06 hour embryonic stages.
Coordinates
chr3R:25677528-25678682:-
Coord C1 exon
chr3R:25678596-25678682
Coord A exon
chr3R:25678538-25678595
Coord C2 exon
chr3R:25677528-25678537
Length
58 bp
Sequences
Splice sites
5' ss Seq
GAAGTATTT
5' ss Score
0.87
3' ss Seq
TCAAAATAAGCTTTGCACAGATG
3' ss Score
-1.85
Exon sequences
Seq C1 exon
AAATAGGTGGCAACCCTAGCACAGCTATGTTTAGTTTTTCTTCACATTTATGGCTAAGAGCGGGGATTTTCAACTGTAAACAAAGAA
Seq A exon
GTATTTATTAGGTAATCTGAGTAATCTTTTCAATTTGATCAAAATAAGCTTTGCACAG
Seq C2 exon
ATGGATCCCCAAACATCAAAAGTATGCCAAACGCTTAATTTTACAATAGCAAGGCGAACTGCAGAAGCTCCCGTGAAGCTTGTATCCCATGAAGTCTCACTTTCAGACAGTACTACTTCTTTGGAGCTGAGCAATTGCTGCCGCTTGTGTTTGGAGGAGCCGTATCCCAACCAAATGCTGGACATGACCGTCATCTATGACCAGGAGGCGGCGCTGAGTTACTACGACTGCTACGAGATCTGCACCAAGGAAGACCTGCGGCAAAATCCCAAAAACGAGCCACGAACCTTGTGCAAACGTTGTGCGGTGGAACTGAAATGGGCCTACGACTTCCACAAGAAAATGGCCATTGCCAATCAGCAGTTGAGGGAGATATTTGTGGCAACCGAAGCCAACACGGAACAGGAAGACGACGTGGAGGATGAGGAGAATGAGGCGGATATGAATGAAGAGTTCCTGATGGAAGAGATTGAGGAGAAGCAGGAAACCCCTATCGACAGCTTAGAGGACATTGTGCCACGCAATCGGCATACGGGAAAATCCAACTGCAAGTTCTGCCACAAGGAGTTCAGGAACCATTCCCGCATGGCCAAGCACCAGATGATTCATTTGGCCAATCGTCCCAACTTTCGTTGCAGCCAGTGCGACCGGGTTTACCTCACAAAGCAGGCGCTGAAAGTTCACGTCGATTCGAAGCACAGGCAGTCTGGAGTCCACTGCGACACATGCGGCAAGGTTTTTGCCATTGCCAAAGCCCTGGAGATTCATAAACGCTATCATAACAGAGACTTTCCCTATTCCTGTGATCTCTGTGATCGTCGTTTCGCACAGCGATCCCATTTGACTGTCCACCAGCAGGTTAAGCACTCTGGATCTCGCTTCATTTGCGAGTTTCCCGGCTGCCAGAAGTCCTTTACCTCATCTTCATCTCTCAGGAATCACGAGTGCACGCATACGGCCATGCCATTTGAGTGCGCCCACTGCCATCAGAGCTATCCAGCTCGTAACAA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0039355:FBtr0084934:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.144
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0777610=zf-AD=WD(100=23.7),PF051298=Elf1=WD(100=22.0),PF134651=zf-H2C2_2=WD(100=7.7),PF0009621=zf-C2H2=WD(100=7.4),PF139121=zf-C2H2_6=PU(57.7=4.5)
Main Inclusion Isoform:
FBpp0303782
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0084308, FBpp0303781
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:
GGCAACCCTAGCACAGCTATG
R:
CTTCTGCAGTTCGCCTTGCTA
Band lengths:
146-204
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)