DmeINT0007207 @ dm6
Intron Retention
Gene
FBgn0014931 | CG2678
Description
This gene is referred to in FlyBase by the symbol DmelCG2678 (FBgn0014931). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 3R:7913851..7916550. Its molecular function is described by: sequence-specific DNA binding; transcription regulatory region sequence-specific DNA binding; zinc ion binding; DNA-binding transcription factor activity; DNA-binding transcription factor activity, RNA polymerase II-specific. It is involved in the biological process described with: regulation of transcription by RNA polymerase II; regulation of transcription, DNA-templated. 14 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: viable; female fertile. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of very low expression. Peak expression observed within 00-06 and 12-24 hour embryonic stages, in adult female stages.
Coordinates
chr3R:7914792-7916453:+
Coord C1 exon
chr3R:7914792-7915274
Coord A exon
chr3R:7915275-7915912
Coord C2 exon
chr3R:7915913-7916453
Length
638 bp
Sequences
Splice sites
5' ss Seq
GCCGTGAGT
5' ss Score
8.56
3' ss Seq
TTCTATTTATTTAACAACAGGAA
3' ss Score
6.98
Exon sequences
Seq C1 exon
AAGTACCAAAATGATCTGCGATGCCGATGGCTACTACAACTGCCCGCACTGTTCTAAGCGATTTTGTTCCCAGACCCAGTTAAGGACCCACATCACCGATCTGTGCAACAGGTGTCCCTACTGCCCACGCACTTATATGCAAAAATCGAACCTCAAGCGGCATTTGCGAAACCACCTAAGCAAGCCAGCGCACAAGTGTTTCCACTGCTCGAAGGCTTTCATGCGTAAAGATCACCTTAAAAGGCACCTGCGCACCCACGACAGTGACGGTCCGCTCTCCTGCAGCCAGTGCTCAGCGGTATTTATCGAACACGTTCAGCTGGAAATCCATCGCAGAGAGCACAAACAAAGGCCGGGCTCTTCAAAATCGGAGTCCACGAAGGATCCTGACTCGGACGACAGCGATCAAGCGCAGGATCTAAAACCAAAGTGGACTAAGAACACCTTCAATGGCACGTGCAGCATTCCACCTATGCTAAAGCC
Seq A exon
GTGAGTTTGGAACTCCACCAGTCTTATGTAATATAGTTATACCTGATAGTTATACTTATACCCTAGTACCGCTGAGAAATTTGTGACGAGCGAAGGTAGCGTATCTGACCCCTTTATATTCTTAATCGGAACCACTAGCCGAGTTCATAAGTTCTCATCAGTCCGTCCGTTCGTCTATTTTTCCGTCTGTCTGTCCGCAGAGATCTCTGGAATTAAAAATCTAGAAAATTAAGGTTTTGAGTTTGTTTCAGACCTTTAAAAAGCCAACAAACGGACATTAAGTTATTGTTTTCATTTATTCTTTTACTTAAATTTTTGGCGATAGCCATTTCGCCGAAGAAAATTTGAATAATCAAACTTTAACCAAACTTTAAAATTGTATACCCGTTACACGATAAGTAATAAAAAGGTTTACTAGTAGAAGGAAATAATAATCTTGCACAGGATCAATAGTCTGTCCGTCCGTCTGCGTGTCCGTAAGAACGCCGTGATCCCGTTAACTATAGGAGCTAAATCCCTAAGATTTAGTAAAATTTATAGAAATAGAAAACCCTCGCACTTTTACTAGCTGATTAACGGGTATCTGATAGTCGAGGCGAATCAACTAATATCATTTGCTTCTATTTATTTAACAACAG
Seq C2 exon
GAAACCGATATGCGATATTTGCCAAAAGAAGTTCAGTAGTGTCTACGCCTTGAAGCGGCATATGCTTACTCACAATCGCCAACATCATCTTAAAAAATGTACCTATTGTTCCGAGGAGTTCAAAACAGAAAAACATCTCAAAAGGCACGAGCGTGGTCACATGGGAGATCTGTTTCGTTGCGAATTTTGCTCATTGGTATTTGTAGATGTTAACTACTTGCGAAAGCACAAAAAACGCATTCACAGCAACAACGTAATAGCGATGTAGGAGAAGATCATGTCCAAACGGGTGACTACCGGTTATACTCTTGGAAAACAACCATTGAATTAAGCAGATTAATATATGTGAAAGGAATATAAACGATTTATTATTCATTATAATTATAATGACCGCAGGTCTAAACTTCTGTTGTTGATTCTTACTTTGAATTTTCTTAAATATGATTCTTTTGTTACTTTCATAAGCTCAAAATTAATATTATTTAAGTTTCGTTTTAATTATATATTTCACAGAAACTCAAATATACTGAGAATAAGCTCT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0014931:FBtr0081757:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.295 A=NA C2=0.047
Domain overlap (PFAM):
C1:
PF0443811=zf-HIT=WD(100=13.6),PF138941=zf-C2H2_4=WD(100=14.2),PF0009621=zf-C2H2=WD(100=13.6),PF134651=zf-H2C2_2=WD(100=15.4)
A:
NA
C2:
PF138941=zf-C2H2_4=WD(100=25.6),PF0009621=zf-C2H2=WD(100=25.6)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0081254
Other Inclusion Isoforms:
FBpp0293246
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:
CAGCTGGAAATCCATCGCAGA
R:
CGCAACGAAACAGATCTCCCA
Band lengths:
349-987
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)