DmeINT0016494 @ dm6
Intron Retention
Gene
FBgn0032083 | CG9541
Description
This gene is referred to in FlyBase by the symbol DmelCG9541 (FBgn0032083). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 2L:8970520..8975428. Its molecular function is described by: nucleoside diphosphate kinase activity; ATP binding. It is involved in the biological process described with: nucleoside diphosphate phosphorylation; purine nucleotide metabolic process; nucleoside triphosphate biosynthetic process. 7 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: viable; fertile. 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 late pupal stages, in adult male stages.
Coordinates
chr2L:8973225-8975428:-
Coord C1 exon
chr2L:8974910-8975428
Coord A exon
chr2L:8973537-8974909
Coord C2 exon
chr2L:8973225-8973536
Length
1373 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
ATTTATTTAAATATAATTAGATG
3' ss Score
3.23
Exon sequences
Seq C1 exon
TTCGGACGTTCGTCGAGTTGTACGTGCTCGGTTTGTTGAACTGCACAACCGCTGAACCGCTGAACTGCTGAACTGTGGCACCGTGTAGCGCACTCGGAAATCGAAAATCGGTACACAAATCGGTCGAGTTCGCGGCTAATGCAGGAATCAAAACACTAAAACCGGCAACGTCATGTAGTTCGTTGTGGTGCGTGTTGCCGACGATAAAGCGCGAGAACAAGTATCCCAGAGATACCAATAATAAATGTACACATATTTATAATATATATCGAGCGAATTTCACTCACGGTAGTCATGGACAGTCGAAGTTATAGAATGCAAAACATTTGTGGAATTCTAAACAATTTCCATTGAGAACTGATCCTTCTTCTACTTTTTATTTTCAACGAGATAATCATTTTAAAGTTGCAAGTGTGTGGGCTAGAGTGTGTGTGGGTGGTGTGCGGTAGGGAAAACACTATTGCGAAAATTCAGCTATACTGGCCACCGAATGGATAATGGGTATTTGTTTAGACACAG
Seq A exon
GTGAGTAATGCCACATGCAGCAGATTTGTAATCAAAGATTAGCATTGCCTCTCCACGGCCAAAGATAACAAAAAGAACCCTAATGAGTCGCGCAGGCGAACACGACAGGTGAAACACGGTATAGAAACTTCATGGGTTTTTGTGACCACGAATTTTCAATGGCAATCAATTAAAGTCGGTCTACATGTATAGAATAGCTTCTAGCTGATCACTGAAAAATATTAACTATTTTGCAGCATACTTTCGGGATACCATTGTTGGTTACATGAACTATATAAATTTAAAAGCAATATAGGAACAGAAATAAAAATTGACTACAAAATGATCCCCATATCATAACGTAACTCTTTTTAGTCTCGGTGACATATTCAATTGACCACAACTCAAAGGACAGTTTCAATTGAAATTACTGCAATCACTTTGCTTGAAATTTATTGAAAGAAAAAACAATTATCTGTGACAAAACGTTGCTTTTATATGTGTACACCTAGCGTTATATCAAAATCGAGACCTTGCCCAACGGTATAATTTGTATCGGAACTTGGACTCTTTTGGCCTCCATGGCTGCCAGGTCCTTGGACATGTTCGTTGACCACCGAAGCTAGTACACATAAATCCTGAAACTAGCGTCACGCACAAAAACAAAAAGAATAGCGATACAAATGGGGAAATCCCCGAGACGAAAAGGGATAGCAACAATAACAAAACATGTCAATTAAATAAAACTGCAGGAAAATCAATAAAAATGTCACAAGGACTGAACTGGTTCCGCGGGTGGGCAGACGTAAAATTTCTATGGGGAAATTTAGAGGGGTATGTGTACGGTATTGAATGCTATGGAATCGCCATGCTGCAGCTGATTTTCCATGAATGAATTCAGCGGTGACGCCATTCTATACTAAACACGGTTGCCATACAATTAAATAATTGTTAAACATGTTTTAATGATGGGCTTTGCGATTTGTTTCGATCCCTAGCTCCCTTCCACCCATCGAGTGCGTGTGGTTTCTGTCACTAATTTCCTACTCCTGGCAAATTGCTTCCGGCCTCGGTGAAGGCTGGCTAATGGCTAATGCCAACTTGGCACGTTATGTCTGCCCTTGCCTTTTTCCGGTCCCCGGTTTCCTTGCGCTAACTTGCCAACACATCCGGTTTCCGGTTTGAAAAATTTCTGCGCTTTTGCCGAAGTCAACTGTTGCTTCTCCATGGGTTTTAAAAACACTTAACTAATGAGATACAGTCCATTAAATTGCCTGTAAAAATCGGAGAATTGGTATATTATTGCTTTCTATTGAATATTTAATTTAAATTCCGTATTTTAGACCGATTACATTTTATTGTAAATTTAAAATAATTTATTTAAATATAATTAG
Seq C2 exon
ATGCCAGCGCGGCACAAGATACCGGCGAACCAGGCAACGATTGGAATCTTACACGGAATCGAAATGGCCAAAATGCTGGCGATTTGGAGGCCGCTGCGGCGGCAGGACGATTGGGTTCTACCAATGTCGGCGCTATCGATATGCAAAATGCTGGAAAAATCAAATTCGATCCGCCCAAAGTGCCAGTGATATTTGTTTTAGGCGGCCCCGGTAGTGGCAAGGTCACCCATTGCGATACCTTCATGCAGGAGCGACGCGGTGTAACGCACATCAATATGATGGATCTCCTCCAGCAATATGCAATGGGCAATG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0032083:FBtr0332206:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.125 A=NA C2=0.333
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0040617=ADK=PU(26.9=37.1)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0304516
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0304515
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:
TAGAGTGTGTGTGGGTGGTGT
R:
CGCTCCTGCATGAAGGTATCG
Band lengths:
351-1724
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)