Special

DmeINT0021527 @ dm6

Intron Retention

Gene
FBgn0001215 | Hrb98DE
Description
The gene Heterogeneous nuclear ribonucleoprotein at 98DE is referred to in FlyBase by the symbol DmelHrb98DE (CG9983, FBgn0001215). It is a protein_coding_gene from Dmel. It has 7 annotated transcripts and 7 polypeptides (4 unique). Gene sequence location is 3R:28599834..28605777. Its molecular function is described by 7 unique terms, many of which group under: heterocyclic compound binding; organic cyclic compound binding; binding; nucleic acid binding; RNA binding. It is involved in the biological process described with 9 unique terms, many of which group under: reproduction; visual system development; female germ-line stem cell population maintenance; stem cell population maintenance; developmental process involved in reproduction. 35 alleles are reported. The phenotypes of these alleles manifest in: fat body; epidermal cell; skeletal muscle of thorax; larva; intracellular membrane-bounded organelle. The phenotypic classes of alleles include: increased mortality during development; phenotype; visible; flightless. 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, at stages throughout the pupal period, in adult female stages.
Coordinates
chr3R:28603608-28605095:+
Coord C1 exon
chr3R:28603608-28603698
Coord A exon
chr3R:28603699-28604060
Coord C2 exon
chr3R:28604061-28605095
Length
362 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
CATTTATCGACATTTTATAGGTG
3' ss Score
6.86
Exon sequences
Seq C1 exon
GCGGTGGCAATCAAGGCAACTATGGCGGAAACAATCAGGGCTTCAATAACGGTGGCAACAACCGCAGATATTGAGAGAGATTCCGGACGAG
Seq A exon
GTGAGACATCCAAATAACCACTACTAACACAAAAATATACATAGTCCAAGGCGAATTCAGGCCATAACTAACCGCTTATCTATCCCGTATGACCATTAATCTTTCGCTTGATTTGACAAACATATGTTGTGTGTTTTTTTTTTTTTATAATAGCGCCCTTATCGGCATTTTTGGTAGTTTATAAAGCATATTGAGACTAAAAAGCAAAACGGCTGAGACAGTCCGACCCACCTTACTCAACAAACTTATATACGTATTTACACTTTTAAGTATTTAGAGAACAAAAACCCATCAACCAATTAAGAACTCCTTTTCATACCAATTGTTTTAAATAACGTTTCTCATTTATCGACATTTTATAG
Seq C2 exon
GTGATAAAGTAAAAGTCGCTCAGTATAATCCCAAAATTCAAAGTCAAGTAAACGATACGCAATTCAATGATCAATATGATGAAGTATGAACGCACGTTCATAGTCCTAAGAAGTTTTCCGAGCACCACAAACCAAACATTACAGATTGATTGATCAGGATCAGTGCAGTGCAGTGAAGTCGTAAGAAGTTTGGTTCAGTCTTGGATTAGAACAGAAAGAGAGATCAGTACCAAGCAAGACCAGACCAATACAGAGTGCAGTGCAGTGCAGAGCAGTGTGTGAGCTAAACAGAAGAAACACAGCAAGTGGCAGTACACGTACACAGAAGGTGACCAGGATTCCATTCAATTTGTCTTTGCAAGCGATGATAAATTGAATGTCAAGAGGCGCATCGAAAACTATCCAATACCCACAGAATTGTAATCTATAATTTGCAACCCATATGTAGCAGCCCATATAAGTAACATTGTAATTAGATCCACAAAGCCGACGACAGGCCAAACATTTGTATCTCCACCACACGAGCAACCAACCAACCAACCTACTTAAAACAACCAGTCATAAACGAATCAGCTATGTAAAACTTCAAGGCGGCAGCCGAGAGATATGTTTCTTTGGTTGCAGACAGCTCTCCAGTCCATCGGCTGCCGGCAACTTTTGATAATCAGAGCAGAAAACACAAAATATATAAAAACATGTATTACATTTTACAACTTTACTAGGCTAAGTTCTCATAGAATTAAATCGAGTAGAGCGTGCGGAGCGACTTCTGCATCCATCCGCACGCTACCCTAGTCTTAATAATTTTACTATTCAAGTTCTAAGCGAACCTGACCGTGTGTGGAGGAATCTAGATACTTAGATTTTTGAATAAGTGTCGACATGGATATAACCTCTTCCGCTGCTTAGATGTAACCGATCAACAAACAACCTTTATTGTAATTTATACCTTTTAGCAAGCAGTCTGTCTGAGGAGTCAGCGCAATTATACTTAACAAAATTTACATTTTAATGTAGCTAAAAAATACAAGATGC
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0001215:FBtr0085298:5
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:
FBpp0084667, FBpp0084668, FBpp0084669, FBpp0084670, FBpp0084671, FBpp0084672
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:
TATGGCGGAAACAATCAGGGC
R:
TTAGCTCACACACTGCTCTGC
Band lengths:
358-720
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)