DmeINT0002015 @ dm6
Intron Retention
Gene
FBgn0036294 | CG10654
Description
This gene is referred to in FlyBase by the symbol DmelCG10654 (FBgn0036294). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 3L:12505374..12507840. Its molecular function is described by 6 unique terms, many of which group under: binding; nucleic acid binding; DNA-binding transcription factor activity; transcription regulator activity; sequence-specific DNA binding. It is involved in the biological process described with: regulation of transcription, DNA-templated; regulation of transcription by RNA polymerase II. 10 alleles are reported. The phenotype of these alleles manifest in: wing. The phenotypic classes of alleles include: viable; visible. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of low expression. Peak expression observed within 06-18 hour embryonic stages, during early larval stages.
Coordinates
chr3L:12505764-12507840:-
Coord C1 exon
chr3L:12507228-12507840
Coord A exon
chr3L:12506488-12507227
Coord C2 exon
chr3L:12505764-12506487
Length
740 bp
Sequences
Splice sites
5' ss Seq
ATTGTGAGT
5' ss Score
7.35
3' ss Seq
TAATACCCTAAATTTTCCAGGAG
3' ss Score
5.42
Exon sequences
Seq C1 exon
CCGCTGGCATTACTGCCATCGTTGGCTTGGCCGCTGGACGCCGGACTGCTGCACTGCCGCCGTCGCAGATTGTGTTAATTGATTTCAATTGGCTCCACGCCATTTGAGTGGCCCGTTGAATCTCCCGACGATGCCAGCAACGATGTTTGATTCCCAGCTGAGTTTGTGCGCGGGTCGCATTGTCGCCGATTCCACCACCACCACTACCTCCGGCATGGATGGATGCGATGGTGCCAAGACGATGATATGCCGCGCTTGTCTTGTGCTACTGGGTCCGCAGGATGCGTGTCACAATCTGGACAGCGAACAGGATCTGGCCAGCAAGTACTACGGCTGTACTGGAGAGGATGCCGTTAGGGATTTGCCACCCCAGTTGGTGCTGAAAAGCATCTGCGAGTGCTGCTATCAGTTGGTGCAAAAGTTCCACGACTTTCAACGCATGTGCGCAGAGTCCTTGCGCAATTTTGAGAAGCTGCTGCAGGACATCGACATCGGATGCCACAAACTGGAGGACCACACTTGGCACGACTTGGACACCCCCTCGGAGAGCAACGAGTCCACTAATCCGGAAGCCCAGTCGCACGCACCCTGCATCGCAGCGACGCAGGAGATT
Seq A exon
GTGAGTTTTATCTGGCCACAAGTGTGCCTGCCTCTGGCCGTAATCTTATCTAGAATCACATTGGGTGCTTCGCTCGAGGTGTGTTGCCTAGCAGCCAAGCAAAGACAATACTGCTCCCCATTCCCCGCCATAAACAAAAACATTTCGACAGCGTTTGTTTGTGTTGTACTATTTTTGTTTGGTGGGTGATAGCACTCGAAAAGGAGGCACGTCCCAATCTATTGGGTATTTTTAAATTTTCCACTAATAAAATTGGGAAGATGGCAACACGCCTCGATTTATGGCTCCTCCAAATAAGAAAGTCGATTTTAAAGGCCAGTTTTATCTAGAATAGATAAATGTGTTCCCTAACTTTCACTCATTTTAGATATTATTTATAGCGCCTTTAATATTTTTAGCATTAAAAAACTAAACTAAACAGATAAGTGACCGCCAAAAGTTCGGTTCACAAAATATTACTTTCATTTTATCATCTTCTAAGTCGAGCGATAAGATAATCTTAATAGCAAATTAAGGAAAAATTTCCACTTTAAAGTAATGAGTAAACATAATGTAATTCCTACCCTTACTACAAATTACTTAACTCAACCAAAAGCAGTTTGTTTTTATATGCTTAGACCCTTTTTACATAAAAAATTCCTTCATAATAGATATGTACAGAATTCCCACAAAAAAAAAAAAAAACCACCACCATTCAGTTTGCTATGGTAATTAAATATATAATACCCTAAATTTTCCAG
Seq C2 exon
GAGGAAGTCTACGTAATAGAGGACGAGTCAGCCAAACAGGATCTGGGCCAGGAGAAGCTATCCATTTCTAGCAAGTTGCTGGGTGCCAGAAAACGACGAGGAGTGCGACACACCCTCGAGTGCCGAATTTGCCACCGTGGCTTCTACAAACCGTCGCTGCTGGAGGCCCATATGCAGCAGCATGAGGGTCTGAGACCGTATACCTGCGTCCATTGTGCCAAGAGCTATGCCCGGGCCAATCTGCTGGAGTCGCACCTGCGGCAGATGCATAACAATGCCGACGCTGCGCGGATCATCTATGCCTGTCCGAGCTGCAACAAGGTGTACACAGCGAACCGAAGTCTCAAATATCACATGAGAAGGACGCACGAAAGGTATCACGAGTCAGAGTCCCCGGATGCGCGGCACATTTGTGAGGAGTGTGGCAAGTGCTTTGCGCGAAAGGCACATCTAACGCGCCACAAGATGGTCCATGGTAGCGTTGAGGGTCGGAGATACTGCTGCGAATGCTGCGATCGCAGATTCTACACCAAGGAGAACATGGTGGATCATCTGCTGCGCAAGCACGGCAATAAGAATCTGCTGCTCAGATGCAGAAAATGCGGACGCATTTTCCAGAACAGCGTGGAGCTCAACGCTCACGGGAGGAAACACAAAGCGATGGATGTAGTTCAATAATTCGTTTTATTTGTGGTTTCAATAACATCAAGCTAACACAACTGTT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0036294:FBtr0075971:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.115 A=NA C2=0.076
Domain overlap (PFAM):
C1:
PF0777610=zf-AD=WD(100=52.2)
A:
NA
C2:
PF134651=zf-H2C2_2=WD(100=11.5),PF0009621=zf-C2H2=WD(100=10.6),PF0009621=zf-C2H2=WD(100=10.2),PF0009621=zf-C2H2=WD(100=10.2)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0075703
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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:
AGGATCTGGCCAGCAAGTACT
R:
CCCAGATCCTGTTTGGCTGAC
Band lengths:
352-1092
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)