Special

DmeINT0029807 @ dm6

Intron Retention

Gene
Description
The gene arrow is referred to in FlyBase by the symbol Dmelarr (CG5912, FBgn0000119). It is a protein_coding_gene from Dmel. It has 2 annotated transcripts and 2 polypeptides (1 unique). Gene sequence location is 2R:13453640..13483229. Its molecular function is described by: Wnt-activated receptor activity; Wnt-protein binding; coreceptor activity; protein binding. It is involved in the biological process described with 9 unique terms, many of which group under: regulation of biological process; behavior; nervous system development; pigmentation; pattern specification process. 45 alleles are reported. The phenotypes of these alleles manifest in: presumptive embryonic/larval nervous system; presumptive embryonic/larval central nervous system; terminal bouton; epithelium; axon terminus. The phenotypic classes of alleles include: phenotype; increased mortality; increased mortality during development; partially lethal. 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 within 00-18 hour embryonic stages, during late larval stages, during early pupal stages.
Coordinates
chr2R:13481776-13483229:-
Coord C1 exon
chr2R:13483155-13483229
Coord A exon
chr2R:13482085-13483154
Coord C2 exon
chr2R:13481776-13482084
Length
1070 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAAT
5' ss Score
4.06
3' ss Seq
CCTCTCCCTTCCACTTGCAGTTT
3' ss Score
11.75
Exon sequences
Seq C1 exon
CTCAGTGCGGTCACACTGTTCGAAAGAGCGAGACGAAAAACACGGCAACACGGCGGACGGAAAACTCAGTGAAAA
Seq A exon
GTAAATCAAATATTTACAAAACAAAGTAACCACAAAATGGCTGCGCTCGGTCGAATTGCGTTGGTTTAACAACAAATAGCGATGAAACGGCGACGATTAATACACTTTCAACGGGCATAAACCATAGATACTGTGGAATTTGTCGTGCTTTTCGTGTTTGTTGTGCAGCATGCGAGATGTTGCTGATGTTGTTGTTGGAATGTGTATCAAATGGTTCTAAAAACAAAACAAGAGATTTTCGGGCATCTAAATTTACGGCCTGCTTGAAAGACGTTCTGTTTTCCCCCAGTGTGTGTGTGCGTCTGTGCATGTGTGCGCGTGTGTTTGTGTGTTTTCTTCTCACTTGCTCTCTGTTGCTGCTGCATTTTCCAGCGGCAAACGGCGTTTGTTTTGGTTGCGTCGTGAAATTTTCCACTGGAAAGTGCAGCGCTGCGCCTTTCTGGGGGTTGCACACACACGCGCACGCACCGCAATTCGTCGATTGCCGGCTTGTTGCGCCGTAGAAGCGGCGGCAAAAGAGGTTCCCTAATTACCCAGAGTCACCTTATCACTTACAGTATTTCAATTTGGCGACCAGTTGATCGGAGGGGGTGATGGCGGTGTGGTGGCCCTCACACAGTTGCACAATTGCTTATCACTCGCTACTTAACGACAACAACAATTGGTGGCTCGCACACATGCAAACAAGACGATCACACTCGTCAACAAAGAAGCGGGAAACTCAATTGAAAGACTGAAATAACAACAACATAAGCAACAGCTAGCTTACACTACGCAACAAAAGTGCGAGCACGAGGAACTAAAAGTTATTAACTCACTAGTGATCAAAACTGAAATAAATTTGAATTGTATTGTAGTCATAACAGTTGAACCAATATTAATCTATTAAAAAAGATACGTAGAAAGTAAAACAAAAATCCTAAAACCTATTTACTAACAGGCATAACTCTGCAAATACTGTTGTAACTACAAACGAGAGTTCAAAACAAGGGTGTTATTTGATACCCTAGGGAGTGAAAGATTTTCGAGAGCGACCTGTTTTCAAACCTCCCTCTCCCTTCCACTTGCAG
Seq C2 exon
TTTTTCCGTGTGATTACCATGTGCGCCTAACAAAAGACAAACACGATCGGGTCGCGTCATCTGTTGTTTTTGCGCCAAATGTCTTAAAATTCCGGAGATAGTGCTTCCAAAATAAGATGGCTCTCGAGCCATACACAAAGTCTGCTGAAATCGAACCTCAATTGTGCCAAGTTATAGATAATAATGAAGATGTGACAACGAAAGCGACGAAATGCACGAAATCTAACAGCGGAGTGGGCTGGCGACAAATGCTGATCGGCTTTCTACTGATTTGCTTTGGCATCTCAAACAGTTGGCAGTACAAAAATG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0000119:FBtr0087702:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact

5' UTR

No structure available
Features
Disorder rate (Iupred):
  C1=NA A=NA C2=0.031
Domain overlap (PFAM):

C1:
NA
A:
NA
C2:
NO


Main Inclusion Isoform:
NA


Main Skipping Isoform:
NA


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
FBpp0086821
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:
CGAGACGAAAAACACGGCAAC
R:
TGCCAACTGTTTGAGATGCCA
Band lengths:
345-1415
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)