DmeINT0021524 @ dm6
Intron Retention
Gene
FBgn0004237 | Hrb87F
Description
The gene Heterogeneous nuclear ribonucleoprotein at 87F is referred to in FlyBase by the symbol DmelHrb87F (CG12749, FBgn0004237). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (1 unique). Gene sequence location is 3R:13656846..13660531. Its molecular function is described by 6 unique terms, many of which group under: heterocyclic compound binding; binding; nucleic acid binding; RNA binding; organic cyclic compound binding. It is involved in the biological process described with 10 unique terms, many of which group under: reproductive process; response to stress; multicellular organism reproduction; response to stimulus; multi-organism reproductive process. 21 alleles are reported. The phenotypes of these alleles manifest in: larval neuroblast; ganglion mother cell; eye. The phenotypic classes of alleles include: locomotor behavior defective; lethal - all die before end of larval stage; visible; neuroanatomy defective; lethal; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of moderately high expression. Peak expression observed within 00-18 hour embryonic stages, during late larval stages, during early pupal stages, in adult female stages.
Coordinates
chr3R:13657324-13658564:-
Coord C1 exon
chr3R:13658462-13658564
Coord A exon
chr3R:13658298-13658461
Coord C2 exon
chr3R:13657324-13658297
Length
164 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
3' ss Seq
TTCTCCTCTTTCGCAACTAGGTA
3' ss Score
9.58
Exon sequences
Seq C1 exon
GTAACCAGGGTGGAGGTCAAGGCTTTGCTGGCAACAACTACAACACCGGAGGTGGTGGCCAGGGTGGAAATATGGGAGGCGGCAATAGACGTTACTAGACAAG
Seq A exon
GTAAATATAGATAACCTGGACGACAGGTCCTATCCCATCGTACAATCTCAAACGCTCGGATCTTTGGTCGTTATTGGCAGCTAGTTGGTAGCCTAGCCATGCAATCAAACTCATTTCGGAACGATTCGAAGCTAATGCAAAATTTTCTCCTCTTTCGCAACTAG
Seq C2 exon
GTAAACACACATAGAGAGAGAGAGTGTGTCAGTTCAAGCTAGACGACAAACAGGCAGTCTAGGCAGGCAGATGCAGAGGGACAAGCACATTCACAGGCAGGCAATCAGTAGCATGTGTGTGTCAGACCAGGCAGACAAGATCAGAACCAAGAAATCAAGATGCAGAACCAAGAACCAGGCCGTGCGCAAATGCAAACGATAAATCAATCAATCAGGTTTGGGTCCGGCCGCAACCTGCAGGCTATAGCCATAATCCACTTGTCAAAAGCACCAAGCAAATGATTATGCGTCAAGCAAAACAGCCAAAAGCGAAACGAAACGAAATCCAATCGACGCCACTTGTCCACAGTTTGAATGCTGCTATCTCTCTTTTGTAACCATTAATAATTCGCTGATCGATTTATGTTTAGGGTCCTAAGAACCCCGAACGCTTAGTTTTAACCATAAACAAACAAAAGAAACAAACACAACAAAATATAAATTAAACAATAATTTTATTGTACAAAATTGACTACCAACTGAGCGGCGACGGATTCTCCTTGAGATTCAGTCGTTGTAAGGGTGTTATAAGGTAGAGCACTTTCTTTATATTTATTCATGATTTTATTGTTTTTAGCGATCCAGCGAAATGTAAGAAATCAAATAGTACCATATTTTGTAATCACTTTTTTTGTACAACTAAGAACCTTTATGATTTGTGGCAAGTAAGATCCCAACTCCTGAAATGCGAATGCCACGCACATTTGTGTACAGGCTGCACAGTGGCCGAGAAATGGTGTCCTAGCGAGCAAAATCCATATATGCATACCAACTCTGTTAGTCCCTAAGAAGTAGATGCTACGTTAAGCCAGACTAAAAAGAAAAACGCTAAACAAATATCACAAACATTCTGTAATTAGTTCGTTACGAGTGAAACGAAAGCGACAAAGAGATACAAGCAAAATAAAATCCTAACCAATGTTACCTACCCACCC
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0004237:FBtr0082851:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0082316, FBpp0289817, FBpp0302741, FBpp0306562
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:
GTGGCCAGGGTGGAAATATGG
R:
TATCGTTTGCATTTGCGCACG
Band lengths:
250-414
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)