Special

DmeINT0029798 @ dm6

Intron Retention

Gene
Description
The gene armadillo is referred to in FlyBase by the symbol Dmelarm (CG11579, FBgn0000117). It is a protein_coding_gene from Dmel. It has 7 annotated transcripts and 7 polypeptides (2 unique). Gene sequence location is X:1891401..1900646. Its molecular function is described by 8 unique terms, many of which group under: binding; protein binding; transcription factor binding; enzyme binding; transcription regulator activity. It is involved in the biological process described with 35 unique terms, many of which group under: compound eye development; sensory system development; eye development; protein localization to adherens junction; regulation of biological quality. 147 alleles are reported. The phenotypes of these alleles manifest in: presumptive embryonic/larval central nervous system; cellular anatomical entity; adherens junction; anchoring junction; tracheal tip cell. The phenotypic classes of alleles include: phenotype; short lived; cell migration defective; increased mortality during development. 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 at stages throughout embryogenesis, during late larval stages, at stages throughout the pupal period, in adult female stages.
Coordinates
chrX:1893403-1894780:-
Coord C1 exon
chrX:1894508-1894780
Coord A exon
chrX:1893500-1894507
Coord C2 exon
chrX:1893403-1893499
Length
1008 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGT
5' ss Score
9.73
3' ss Seq
ACGAATTCGATCGATCACAGGAT
3' ss Score
4.02
Exon sequences
Seq C1 exon
CGCGTGGCTGCTGGCGTTCTTTGTGAGCTCGCCGCTGACAAGGAGGGCGCCGAGATTATCGAGCAGGAGGGCGCCACTGGGCCGCTGACCGATCTCCTGCACTCGCGCAATGAAGGCGTGGCCACATACGCCGCCGCTGTTCTCTTTCGCATGAGTGAGGACAAGCCGCAGGATTACAAGAAGCGGCTATCCATAGAGCTGACCAACTCGCTGCTGCGCGAGGACAACAACATATGGGCCAATGCCGACCTGGGCATGGGTCCCGATCTACAG
Seq A exon
GTGCGTGCTAAGTAGGCTAAGCAAATTCGACGTCCCCGGGATTCCGGCTTTTTAAACGCCCTTCTTGTGTTCCATTGAATCTGATTTAAAAATGCAGCGCGTTAAGCGAAATCTGTACATAAAATTGTAAATTTGTAGAGAACCTACTTTAGTCAAGCATTATATAATGGTATCCAGATTAAGTATCGACCTATATATCGCTTGCTTACGATTTCGATAACCTATTTTTGAATTTCCATTTCATTTGGGTTCATTTCGTTCGGTTTTTTGCTTTTCTTGTAAACCACCAATCGATAGACCGTATATGTTAGTCGATAAGTAGGTAGTTGTAGATGAACGCCGATTACAAATACGGATTCCGATTAGTTCTGATCATATTTGATTGATACCCTCCCCAAACCACACAACCCAACCTCACCCCCTCCACGATTCCTCCGAAAACAACCCGACCAAAAACATACTTACATGAATTTCAATTTGTATAATTGCTGCGTCATCGCGCTCTTTGTTTATGTTTAATTTTGATTTTGTAATTAATTCACGTTTGTTTTACTTTTGTTCTTTTCTTTTTTTCCTTTATGTTTACTTTGTGTGTGTAAAACCAAAACAACCCAAAACAAAACAACAAATCACTATAAACACAACTGCAACGGTAAATGAAACGCAACAACAACCGAAATGACGGATAATCACTGCACCAAAATCTCACCAACAACAACAATCCAACAATGCGACTCTCACTCTCTGTCTCGCTCTCGCCGCCCCGATACCACAACAACCTCACCCCACTCTCTATTCCTCTCGCTCACATTCACTTGCAAACTGGCGTTTGCGCGTGTCTTCTTCTTTCCTAACAACTTTTCACTTCTGATCCATCCCAACAAAAAATAAATGAAAACGAAACTGTAAAAAATACATCCACCACACAACCACACACGTACGATCACGCACATATCACGCAAACCGACCGATAAACCGATAAACAAACACGAATTCGATCGATCACAG
Seq C2 exon
GATATGCTTGGACCAGAAGAAGCATATGAGGGCCTGTACGGACAAGGTCCGCCCAGCGTGCACAGTTCACACGGAGGTCGCGCATTCCATCAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0000117:FBtr0089991:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.136 A=NA C2=0.970
Domain overlap (PFAM):

C1:
PF0051418=Arm=PD(26.8=12.1),PF0051418=Arm=WD(100=45.1)
A:
NA
C2:
NO


Main Inclusion Isoform:
NA


Main Skipping Isoform:
FBpp0089031


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
FBpp0089032, FBpp0089034, FBpp0089035, FBpp0304835
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:
CTGGCGTTCTTTGTGAGCTCG
R:
CGACCTCCGTGTGAACTGTG
Band lengths:
343-1351
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)