Special

DmeINT0035125 @ dm6

Intron Retention

Gene
Description
The gene proboscipedia is referred to in FlyBase by the symbol Dmelpb (CG31481, FBgn0051481). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (4 unique). Gene sequence location is 3R:6707800..6742063. Its molecular function is described by: RNA polymerase II cis-regulatory region sequence-specific DNA binding; DNA-binding transcription factor activity. It is involved in the biological process described with: specification of segmental identity, maxillary segment; proboscis development; positive regulation of transcription by RNA polymerase II; specification of segmental identity, labial segment. 98 alleles are reported. The phenotypes of these alleles manifest in: primordium; stage 7 embryo; early extended germ band embryo; embryonic midgut chamber 1; prothoracic ventral intersegmental muscle. The phenotypic classes of alleles include: lethal; visible; lethal - all die before end of pupal stage; short lived; some die during pupal stage; wild-type. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of low expression to a trough of extremely low expression. Peak expression observed within 06-24 hour embryonic stages, during early larval stages, at stages throughout the pupal period.
Coordinates
chr3R:6739550-6742063:-
Coord C1 exon
chr3R:6741168-6742063
Coord A exon
chr3R:6740175-6741167
Coord C2 exon
chr3R:6739550-6740174
Length
993 bp
Sequences
Splice sites
5' ss Seq
ATGGTACGA
5' ss Score
7.82
3' ss Seq
AAAATGGCTTTCCTTTCCAGGTT
3' ss Score
9.74
Exon sequences
Seq C1 exon
GGTGCTATTGGATGGAATGGTTGTTGGCTGCTATCTAGCTCTCGGGAACCGCACGAAGCTCCCCAAAAGCCCTCTGTCTCGCTCTCGCTACGAATCGGTTCGGTATCTAAAAAATAATATTTATTAAAATGACAGCTACAAAAATAGTTCAAAAATTTTGAAAACTAAAAAGTGATATTATTAAAACGAGTTGAAACCAAAAGTTTTACTATACGGTTGAGAAGCACTTTAGGAACCCCTGGAAACCCGGTTCTGCGCACCTCTTGAAGGCCAGAGAGGGACAGCTAGTGCCCACATGTGTATGAGTGCGAGTGGAGAAAACTATCTCAGACGAATTGCAACGACTGAGTGTGTGTCTGTGTGTGGCCATTGCAGCGATCGCAGCGACTCTACAAAACTCTACAAAATCAACACATTCCGCATACGCACCGTTGTACAGCGCGTACTTGCACTATTGTCGTTATCGCCGTTGTTTCGTCGGTTGTGTTGGCCTTTCGCGTCGCCATGGCTGCCAAAAGGTGTGTGTCTATGTCAACCTGAAAGCGAAAAACCAACTCCAAACACCACTTGACGGTTGAGCAAACACAACGGTGGCCATATTTACATTCGGATCTGGGTTCCCTCGCTCTCGTCGCGGTTGTCGCCTCTTTTCGCGGCCCACAGATAAGCCCTGACACACTGAAGTTTTACGCAAAACCCGCATCGCAAAAGTTGTGCCGGTTGAAACTAAAAAAAAAAAACAAACAAAAAGTTAAGCCAGTTACTATGAGCGAGTGCAGACAATAGTGAAAACGGTGACCCAAGTGATACCGGTGAAATTTCCACAAAGAACGCATATGTCAACGTAAGAGGAGAAATATGGAATACTGTGGTCTGTAAATGATCAACTTAATATG
Seq A exon
GTACGAAATTATCTTACACATATTTCTTACCTACATTTAAAAATAAGTGTATCCTTTTAAAGCACGAGAAAATCAAAGCGTGTCGTTATTTCGTTTTTGATACAACATGTTAGTCTAAAATACGAGCCTTTTAAGTCGGCAAAATGTTTACTGCAAGAAATATTTCAAATCTTTAATTGGCGGAATCGGAAAATATATTCGAATTTTCTTATTCATTTATACTTCCTAGGAAATTAGCTATGCGGCATTTCTTAGATGAGGATATGTAACAGCTTTATAACTTTTTCTGTTTAAAATATGTTAATTTATTTACTGACTATTAATCCTTAAAAAAATAATGTAAAATAATGTATGCGAACCAAGCCAATTTAGGTAACATTGTAGGACAGGTTGTATGTATTGTACATACATACAATACATATTGTCAAATCTCAATCGAAATTAGGTGGCCATAAATTTAAAGTGAAGGCCTAACAATTTCTATAAGAGCAATAGTAAAAATGCAGACTACAAATGAATTTCTGGCACAGAAAACTGAGAGACTAATGAAATATAAATTGGAATATGTAATTTAAAAATAGTCAAGTTTTTGACAGTTGCAATGTGAAAAATTGGATCGGTAATAATAAAATAAACATTGATTAGCATAGTAAAGTGACGATGTTTTTGTTTCTTAAAATGTTAATGAAGATAATGACATATCTTAATGAAGTATATACGTACATTATATTGAAATTATATATATTCAAAATATATAAATAAAAATTCAAAAATTATAAATATAATAATAAAATAAACATTGAATAGCATAGTAAAGTGACGATGTCTTTGTTTCTTAAAAGGTTAATGAAGATAATGATAACATATCTTAATGAAGTATATACATACATTATTCAATTTCACATTCGATAAGAACAGTGAAACCTCTAACTTCCTGGGAACTGAATCGTGATAACATTATTATGAGATTACAAAAATGGCTTTCCTTTCCAG
Seq C2 exon
GTTCCCAAGCTGAGGAACATCTAATACGCTCAGGAATTGAAATAGAAAGAATCTAAAAAAAATTATACCCAAGCTATGCAAGAAGTCTGCAGCTCCTTGGACACGACCTCAATGGGCACCCAAATCAAATCGGAATCTCCACTCAACCCGCTGCAGGTGCAAACTGGACAGACGTCCCTGCCAGTGGGTGGTTGCGGTGGTGCGGGCGTCGTGGGTGGTGTGGGTGGCGTGGGAGTGAGTGTTGGTCAGCCTGGTATCGGACAGCAGGGGGTGCCACCTGTGCCGTCGGTGCTCATGGTCAACAAGATGACCCCGAACTGTGATAAACGGAGCGCGGACACGGCCTATTGGATGACAGCATCCGAGGGCGGGTTCATCAATTCGCAGCCGTCGATGGCTGAATTCCTCAACCACTTGAGTCCGGAGAGTCCCAAAATCGGAACACCTGTTGGATCCGGCGCCATTGGCGGAGTAGGCGTCAACGTTAATGTCAATGTCGGCGTCGGAGTCGGATATCCGGTTGGCGTTGTCCCTCAAACGCCGGATGGAATGGACTCGGTGCCGGAGTATCCCTGGATGAAGGAGAAGAAGACATCCCGCAAGAGCAGCAACAACAACAATCAGG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0051481:FBtr0089276:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact

5' UTR

No structure available
Features
Disorder rate (Iupred):
  C1=NA A=NA C2=0.556
Domain overlap (PFAM):

C1:
NA
A:
NA
C2:
NO


Main Inclusion Isoform:
NA


Main Skipping Isoform:
NA


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
FBpp0088333, FBpp0088334, FBpp0088335, FBpp0088336
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:
AAACCCGCATCGCAAAAGTTG
R:
CAGCGGGTTGAGTGGAGATTC
Band lengths:
356-1349
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)