DmeINT0030543 @ dm6
Intron Retention
Gene
FBgn0000289 | cg
Description
The gene combgap is referred to in FlyBase by the symbol Dmelcg (CG8367, FBgn0000289). It is a protein_coding_gene from Dmel. It has 12 annotated transcripts and 12 polypeptides (10 unique). Gene sequence location is 2R:14173693..14182838. Its molecular function is described by: DNA binding; DNA-binding transcription factor activity. It is involved in the biological process described with: regulation of transcription, DNA-templated; imaginal disc-derived wing morphogenesis. 41 alleles are reported. The phenotypes of these alleles manifest in: adult antennal segment; adult central brain; embryonic/larval digestive system; alimentary canal; imaginal tissue. The phenotypic classes of alleles include: partially lethal; increased mortality; phenotype; increased mortality during development. 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 00-18 hour embryonic stages, in adult female stages.
Coordinates
chr2R:14176612-14178021:+
Coord C1 exon
chr2R:14176612-14176691
Coord A exon
chr2R:14176692-14177860
Coord C2 exon
chr2R:14177861-14178021
Length
1169 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
CGGTGCAACAACACTCTTAGGTG
3' ss Score
1.77
Exon sequences
Seq C1 exon
AGTTATCACTGCCGGCGGAGCATCGACGGTGGTCAAGAAGCAGGACAACAATCAGCAGGTCCTGAGCCTCGACAAGAACT
Seq A exon
GTAAGTGGATCGATTCTAAACGAATCAAAAACCCATCGAATCGATTCAGTGTTGCACGCATTGCTGTTACTGTGTTGTGATTATCTATATATTTTGGGTTTTCTGTTAATCGATTGTTTTTCTCTCTCTACTCCCGTTTATTTATTTAATTAATTTATTTTTTTTTTTAATTCTCGCTCGATCTCGCTCGCCCTTGAATTCAACCCGAAAAACCGAACCCGAAACCGAAACCCAAAATCCACCATCTCCTCCGATAAATCCCATTGTGCTTGTGTGTTTGCCCGATTTTGCTATTGCACCCGATCCACCACCGACCCACCGATCATCTCGTTAACTGCACCGCATAAAAACTACAACATTACCATCTCACCATATAATAACACACACACAACACCTCATCACTTGGCGGGCGGCGGGCGCGGGCTGATCGAACCTTCCTTCAACCGAAATGAAACGTATCAACCCATCGAATTGAAAAAACAGATCTGCTAGTGGATCCGGCCACGGCCGCAGCAGCTGCAGCCGCCGCTGGTGGGGATTCGGGTCTCGCCCACCACCATACGTTGACCAATGGCAGCATTGTTGATGCGAAGACCGGACAGACGGTGCTAACCGCCGGATCTGCGGCGGCCAAGTCGCACTTCAGCTCGATCGGAGCACTGCATCTTACGCAAGAGGAGTGCAACGAGATCCTGATCAAGCGCGCCATCGCTGCCGGCCACCATCAGACGCACACGATCACCGCTGCCGACGGATCCCATCACCATGCGTCCGGCGGGACACCAAGTAAGCATCTCAAATCTGTGTTTGTTACCCCTGATCCAGTCCCTCCTGCCACCTACTCCTCCACACACTACACACTACAATCAGATCTGATCCCCGATTGAAGTAATCCTACCGGAAAATACCCGGCATATTGGTACATTCTCGGTTCCGGTTGCTTTTACCTGGTTGCGTGGTTACGTTGTAATCATAGTTTTTGCCATTGTTTAGTTGGTCTAACATTGTTTTAAGTTTGATTAACCCAATTGAACCCAAATAGTTTGATTTTGCATATTCAGTTTGTTCGGATCTTTGATTTTTTTCCTTTGTTTCTTCTCTATTTTTTTGTATCTTCCTTTGAATTCCATTTGGCTTTTGTTCCGTTGGCGGTGCAACAACACTCTTAG
Seq C2 exon
GTGACATACTTCCTGGTATTTCAGTTCAAGTGCAGAAAGTCATACAAGGACTGGAGGATAACGAGGACTCGCAAGGCGAAGCACCCAACCTAAAGTTGGAGCCAGGCACATTAGAGTTGTCCCCGAAGACCGAACTACAGGAATCAATGCATTTCAGCGAA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0000289:FBtr0087529:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.369 A=NA C2=0.769
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0086655
Other Inclusion Isoforms:
FBpp0086656, FBpp0111707, FBpp0288473, FBpp0288474, FBpp0308983, FBpp0308984
Other Skipping Isoforms:
FBpp0086657, FBpp0086658, FBpp0308982
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:
GTTATCACTGCCGGCGGAG
R:
CGCTGAAATGCATTGATTCCTGT
Band lengths:
238-1407
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)