DmeINT0038468 @ dm6
Intron Retention
Gene
FBgn0004606 | zfh1
Description
The gene Zn finger homeodomain 1 is referred to in FlyBase by the symbol Dmelzfh1 (CG1322, FBgn0004606). It is a protein_coding_gene from Dmel. It has 4 annotated transcripts and 4 polypeptides (3 unique). Gene sequence location is 3R:30765926..30789202. Its molecular function is described by: DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II regulatory region sequence-specific DNA binding. It is involved in the biological process described with 12 unique terms, many of which group under: organic cyclic compound biosynthetic process; mesoderm development; cell motility; negative regulation of muscle cell differentiation; nephrocyte differentiation. 45 alleles are reported. The phenotypes of these alleles manifest in: germline cell; somatic stem cell; trachea; A1-7 dorsal acute muscle 1; intracellular. The phenotypic classes of alleles include: female sterile; phenotype; increased mortality during development; lethal - all die before end of larval stage. 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 at stages throughout embryogenesis.
Coordinates
chr3R:30783258-30785941:+
Coord C1 exon
chr3R:30783258-30783650
Coord A exon
chr3R:30783651-30783942
Coord C2 exon
chr3R:30783943-30785941
Length
292 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACC
5' ss Score
9.24
3' ss Seq
AACCTACCTCCTATTTGCAGACC
3' ss Score
8.8
Exon sequences
Seq C1 exon
CGCGTTCGCTTTTTCTACATTTTCATTGGCGCGTTTAATTGAAGTTTCGGCGTATTTTCATTCGAAAACGTTTGCACAATTCACCAAATATCACAAAATCACAAAACGTCCACTTTTACGACTCAGAAACACACACGCAGCAAAAAATGGCCCGTTTTCCGCGGTCGCTTTGGATTTGGCCCGCTTTTTTGTGGTCGCAGCTCTCGCCTTGAAACAAATTAGAAAGCCATTAAATTTAAAACAAATAAATACGCGTGTTGTTTTAAACAGTTTTTATTACCTGTGCGTTGGTGTTTCGTTTTACCCCTGATTCCCTAAACACGACCCCAAAATAAAGCAACAATGTCGGCGGCCGCTTGCCTACTGTCTTCTTCTACTTCTTCGTTCGAGAAG
Seq A exon
GTAACCGGGAAAAAAACAAAAGATCGTAGAATGGGAGAAATGGTAGAAATATGCGTGGGGAGCGAAAGTTGCCAACTAGAGGTGACACTTTTGAACAGCAAACTATCGGCATTGAAAACTTTTCAAAAATTGATTTAAATATGAGCCTATGTCAAATCAACAAGTTCATTAAAATGAAGAATGTTAGTACTGCGTAACTAGGGATAACATATCTAGTTTTCCTACTACTCTTAGCATTAAGAGTCTCCTTCTCATGTTCCCACTACAATCGCAACCTACCTCCTATTTGCAG
Seq C2 exon
ACCTGCCGCATCTGCCACAAGGCCTTCGCGAACGTCTACCGCCTGCAGAGGCACATGATCAGCCACGACGAGAGTGCGCTGCTGCGGAAGTTTAAGTGCAAGGAGTGCGACAAGGCCTTCAAGTTCAAGCACCACCTCAAGGAGCACGTGAGGATCCATTCCGGCGAGAAGCCCTTCGGATGCGACAACTGCGGCAAGCGATTCTCGCACTCGGGCAGCTTCTCCTCCCACATGACCTCCAAGAAGTGCATCAGCATGGGCCTCAAGCTGAACAACAATCGCGCTCTGCTGAAGCGACTGGAGAAGAGCCCGGGATCCGCATCCTCCGCATCCCGGCGATCGCCCTCCGATCACGGAAAGGGCAAGCTGCCGGAGCAGCCGTCGCTACCGGGACTACCACATCCGATGAGCTACTTCGCCAGCGATGCGCAGGTGCAAGGTGGAAGTGCGGCACCCGCGCCCTTCCCGCCATTCCATCCGAACTACATGAACGCGGCCCTGCTCGCCTTTCCCCACAACTTTATGGCGGCTGCAGCTGGCCTGGATCCTCGGGTGCATCCCTACAGCATCCAGAGGCTGCTGCAACTTTCCGCCGCCGGTCAGCAGCAGAGGGAGGAGGAGCGTGAGGAGCAGCAAAAGCAGCAGCAGCATGATGAGGAGGAGACCCCCGATGAGCCCAAGCTAGTGATGGATATCGAGGAGCCAGAGACCAAGGAGATGGCACCCACGCCAGAGGCCACCGAAGCAGCCACTCCCATTAAGCGGGAGGAGAGCAGGGAAGCCTCTCCCGATCCAGAGAGCTACCGTTCCTCCTCGCAAGCAATCAAACAAGAGCAGGAGCCCCTGAACGTAGCAGAGGAACGTCAAACTCCTGTGGAAGAACACGCCCCCGTGGAGCATGCCGCTGATCTGCGCTGCAGTCGCTGCTCCAAGCAGTTCAATCATCCCACTGAGCTGGTGCAGCACGAGAAGGTGCTTTGTGGCCTGATCAAGGAGGAGCTGGAGCAGCACTTCCAACAGCAACAGGCCACGTCCTTTGCCTTGGCCTCCGCCAGCGAAGAGGACGAGGAAGACGAGGAGATGGATGTGGAGGAGGAGCCCCGCCAGGAGAGTGGCGAACGGAAAGTCCGCGTGCGAACGGCCATCAACGAGGAGCAGCAGCAGCAGTTGAAGCAGCACTACTCCCTGAACGCTCGACCCAGTAGGGATGAGTTCCGAATGATAGCAGCTCGTCTGCAGCTGGATCCCCGAGTGGTTCAAGTGTGGTTCCAGAACAACCGCTCCAGGGAGCGCAAAATGCAGAGTTTCCAGAACAATCAGGCGGCAGGCGCAGCACCGCCAATGCCCATTGACTCCCAGGCATCTCTAACCCGGGAGGATCAACCGCTGGACTTGTCCGTGAAGAGAGATCCCCTCACGCCGAAGAGTGAGAGCTCGCCTCCGTATATAGCTCCACCGTCGGGAGAAGCCCTCAATCCCGAAGCAATCAATCTCAGCAGGAAGTTCTCCACATCCGCATCGATGTCGCCGGCCTCGATTTCACCGTCATCCGCGGCAGCCCTCTACTTTGGTGCTGCCCCGCCGCCTTCGCCCCCAAATAGCCAACTGGATTCCACTCCTCGCAGTGGCCAGGCCTTTCCGGGACTACCTCCCTACATGCTGCCCATGTCGCTGCCCATGGAGGCGCTGTTTAAGATGCGCCCGGGCGGAGACTTCGCTTCCAACCATGCCTTGATGAACAGTATTAAGCTGCCCGATTACCGGGGCACCAGCTTGAGTCCCGGTGGATCGGAGAAGCGTTCGTGGCGGGACGACGACTCGCGCATCTCACACGAGGACGAGTTCGGCGCCGGCGTTCTGATGCCACCGAAACCGCGTAGGGGCAAGGCGGAGACCCATGGACACGCTGGCGATCCCGATCTGCCCTATGTGTGCGATCAGTGCGACAAGGCCTTCGCCAAGCAGAGTTCGCTGGCGCGACACAAATACGAGCATTCCG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0004606:FBtr0085702:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.687
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF138941=zf-C2H2_4=PD(91.7=3.3),PF134651=zf-H2C2_2=WD(100=3.9),PF138941=zf-C2H2_4=WD(100=3.6),PF0004624=Homeobox=WD(100=8.5),PF134651=zf-H2C2_2=PU(38.5=1.5)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0085064
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:
TTTTTGTGGTCGCAGCTCTCG
R:
TGCACTTAAACTTCCGCAGCA
Band lengths:
308-600
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)