DmeINT0003037 @ dm6
Intron Retention
Gene
FBgn0035137 | CG1233
Description
This gene is referred to in FlyBase by the symbol DmelCG1233 (FBgn0035137). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 3L:361472..365681. Its molecular function is described by: DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding. It is involved in the biological process described with: negative 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: visible; lethal; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of low expression. Peak expression observed at stages throughout embryogenesis, at stages throughout the larval period, at stages throughout the pupal period, in stages of adults of both sexes.
Coordinates
chr3L:361472-364903:+
Coord C1 exon
chr3L:361472-362341
Coord A exon
chr3L:362342-362426
Coord C2 exon
chr3L:362427-364903
Length
85 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TTTCACGTGTTTTTCGACAGGCT
3' ss Score
8.96
Exon sequences
Seq C1 exon
GCTGCCACACTGTGTACAGCAACAGCTGTTCGCTATCAGTTATTTTGTGATGAAAAGTTTTTTTTCTGCGTAATGCCAATTTTTGTGATGCGGAATTAAGAGGCGTGTGCCCAGGAAGCGGAAAACCGGCAACCGGCAACCGGAATCCGGCACCGGGAATCAACTGGACCAAGGAAGGCACCCACGATGAGCGATGCGACCTATCCGGGATATTACGGCGGCAACCAGGTGAGCAACCAGCGAGTACCTCTGGCCAGAAAAACACGCCGTGTGTCTTCCAGCTGCTCCCGTTGTCGCATCCGCATCCTACACATCCGCACCAAGACCTGTCGCTTTCCACGCCGGTTCACTCCTTGGAGCAGGACTCCAACTTCGGGGGATTCTTTGACGAAGAGCTGGTCATCGGATCGGGATCCGGATCTGCCTCCGCGTCTGCTGCAAACACCACCCCTTCTGGAACTACTTTGTGGCTGGCCGATGGCGGGAATCGATCACCTACTGAGGTGGCGGTGGAGTCCCAGCCCAATCAGGGCATTCCCTTTGTCCAGATCCACACCACCGACTTGCAGCAACCAGAGAAAAGCTACCGCAATGCCTTCCGCAGGCGTACAGCGGAAATTAAGTCGGAGGAACTAATCAAGTCGGAACTTGCGGAAGCGGCAGCCAAGGATCGCCTGAATGCCACGCCAACGCCACCAACTCGAAATTCCAGCTGCGCCAGCGTGGAGGGCAAGGCAATCATTCAGGAGGGTCCGCCTCTTATCCTGCGCTGTCCTAATTGTCCATTCTTAAGCCTCTGCCAGATGCGTCTTCAGCAACACCTTAGTCAGGGCAACTGCTATATGGAGCAGCACAGGAAACAGTGTCCAG
Seq A exon
GTGAGGCATAGTGCGCCTTCAATATGAGTGCTCTGCTGGAATGCTTCATCATATTTGCATTCACTTTTCACGTGTTTTTCGACAG
Seq C2 exon
GCTGCTCAAACATTTTCTACACCAGCGATGCGCTCAGCTTGCACCTCAGCTTGGACCATCAAATGGAGGACAGTGAGACACTTGCGCTTATGGGCAGAAAAGTCACTGAAGCACAAACTAAAAAGCAGACTCAGATGTCGCAGAGCCAAAATCGACCCAAGAGCCGCATCTTTATAAAAAGCGTAGATTGCCTAAGGGAGCCACTCCCGGATTTCCCGCCCTTAATGCCGGATAGCGGGTCCGCCGCTAACATTCTTGATCTGCTGGAAGGTGTGGCTGTAGGTGCATCGCCGACCGAACAGACAATGCCAACAGCACCTGCTGCGAATTTACCAGCTCCGCCGCCAAAGCCCATCCAGAAGATCTCCATCAAGAGCGTGGACGTGCTCAGGGAGACCGCTTTGCTGCCGTTCGACTTCCAGCTGCAGAACCATTCGGTCAATACGGACAATAGTCTCCCTGAAGTTCCTGATGTTGTCGGGGAGCCGGAGAAGCCGCGCCAGCCGAAGATTTATATCCGCAATGTAGACATCCTCAAGGAACCGATGGTTTTGCCATCTGCTCTGCCCGGTCTGGGATTCAATAGCACCATGCCGTCGGCAGCAGAGCCAGGACAAAGTGGCCTGGTTGTAGGAGGAGCAGATGGTGATGTCTTCCAGTCGGAGACACTACTAACGCCCACGTGTCAGCTTCCAGGATTCGAGCCCAGCCTCGCCCCGCTCGCACAGATGTGTTCCGAGGCATTTCCCTTTGATTCTGTGCTGAATGGCAATGGAGCACCTGCCGCCCATGTGGAAAACACACGTTTTAGTGCTTTGGACCTTGATTTTGGTGTGGATTTTGTTTCGGAAGAGGCAACTCCGCCACCTCCTCTGAATGATCCACTGACAATGATGGAACCACAACCTGTCCAGCTGGAGCACTACATGCCACCTACGGCTCCCATTACGACCAAGCAAAAGATCTTCATCAAAAACGTGGACATTTTGAAAGCACCGCAGAGGGGCACCTTGCACCTGCGCACTGTGGACGAACTAAACCTAATGAATCGCACCGAGGTGGAGCACTTAATCGTGCCCAATCTAGAACCGATGGCAATGACCATGATGGAGCTTCCGCCCGTGCAGCAGCAGCCAATGGAAGTAACTTCACAGCTCAAGGGACCAACGGAAACGCTTGGCGAATTTCAGCCGTCTATTAGTGAAAGTTGGCCTAGCGAGGATGGCTATGACCTACCTGAGGATCTGGAGTGCTGGCCGTGGATGGAAGATGCTGTACCAGAAGCTGGACTCGTTCTGCCTACACCCAGTGAAGTGGCTAATGCTCCCCCACTCGATGGTTTGTCTCACAATGCAGTGGATCTGCTAGTCAAGGATTTTTCGCATTTGTACGCCGCACCACCGGAGGACACACAAAACGCAGAAGAAGGAACTGCAGCGGGAGGACGAGGGACAGTGCCACCTCTAGTACCGGTAACATCTTCGGAAGGGACAGCCTCTGTTGCTCAAAGTGCAGCCTTAGGTAGTTTGCCGGTTCCGCCGCTGGTTCCCTTGGCAGCCGAGATGAATGCTGCTATCGAAAAGCCAGCCCGCATCTATGTGGCCAATAATCTTCTTCCCGCCGCCGTGGACCCACCGCTTCTTGGAGGCGGCACCTCGGTCAGGGGCCGTCCCTACGGAGCGAAGCACTCTGGTGGAGCAGCTTCCAAAAGAAAACTCTCTCTGGGCCCAAATCAAGTGCCAGAGGGAGGCAAGTGCCTTGTGGAGGGCTGTATGTTCCGTTTCAAATCACCCGTAACTTTGGAGTATCACGGCAGATGCCACAATGGATCCCTCAGCTCAAACCAACCCGTTGTGTGCCCGGAATGCAAGTCCAGCAACTTTAGCAATTGGAACTGTCTGCATACGCATCTCTGGCGGACCCACCAAATCGACATGGAGCTGTACTCCTGCCAGCTGTGCAGCTTTAAGACGCCCATCTATTCGCGTCTCGTGAACACCCACGCTAAGATCCACTCGGAGGAGCGAAACTATAAGTGCGAGCAGTGTGGCAAGGGATTTAAGAACACCAAGCAATTGAAGAATCACCGTCGCTTGCATCGCACTCAAGGATTGGGCATGGGAAAGCAGTCGAACGAGCAGATTTCCGTGGGACCAGAAGGTAATCCCGTTGTAATGCATCGCTGCGAAGATTGCGGCGCCGCCTTCAAGCAGAAGAAAACCCTAAGGGAGCACCTATGCAAAGAGCGAAACGAACAGCTGGAATGCCCCGAGTGCCAGCGCCGTTTTGGTTCTAAGAGCAGCCTGAGACTTCATCTTCGGAGCCATCAGGAGCATAAACGTTTCCGCTGCGACACCTGTGATCATGAGACCAGCGATCACAATGCCTATCGCCGCCACCTAGCCACGCACAAGGAGAGTAAACGCTACTCCTGCCCGCACTGCGACTTCCGAGCCATCCAGAGCACCGCCTTTCGG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0035137:FBtr0072549:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.454 A=NA C2=0.390
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009621=zf-C2H2=WD(100=2.8),PF0009621=zf-C2H2=WD(100=2.7),PF0009621=zf-C2H2=WD(100=2.8),PF0403211=Rpr2=PU(59.7=4.5),PF134651=zf-H2C2_2=WD(100=3.0)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0072448
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0072447
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:
CTCTGCCAGATGCGTCTTCAG
R:
TTTCTGCCCATAAGCGCAAGT
Band lengths:
176-261
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)