DmeINT0023554 @ dm6
Intron Retention
Gene
FBgn0015774 | NetB
Description
The gene Netrin-B is referred to in FlyBase by the symbol DmelNetB (CG10521, FBgn0015774). It is a protein_coding_gene from Dmel. It has 8 annotated transcripts and 8 polypeptides (2 unique). Gene sequence location is X:14686038..14749376. Its molecular function is unknown. It is involved in the biological process described with 12 unique terms, many of which group under: cell recognition; tissue development; regulation of cell projection organization; synaptic target attraction; salivary gland boundary specification. 40 alleles are reported. The phenotypes of these alleles manifest in: intersegmental nerve; plasma membrane bounded cell projection; ventral nerve cord; appendage; optic nerve. The phenotypic classes of alleles include: partially lethal - majority die; phenotype; visible; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of very low expression. Peak expression observed at stages throughout embryogenesis, during early larval stages, at stages throughout the pupal period.
Coordinates
chrX:14746573-14748921:-
Coord C1 exon
chrX:14748629-14748921
Coord A exon
chrX:14748060-14748628
Coord C2 exon
chrX:14746573-14748059
Length
569 bp
Sequences
Splice sites
5' ss Seq
AATGTACGT
5' ss Score
6.58
3' ss Seq
TTTTCCCCTTTCCGATTCAGGGT
3' ss Score
11.34
Exon sequences
Seq C1 exon
AATCTAGAGTATCTCGTATCGAATTATCGTATCGCATCGAATCGGATAGACTGAAGCCAAACCTGAGACTGAGAATTGGCAGCTGTTGCATGCTGTTGCGGCAGACTCAGTGACGCCGCGAGTGACGTCGCCGTGTCTTGTTTTTGTTGCTTGTTTGTTTGGTGACCCCGACGCGAATCGATCCTCGCGAGTGTGTGACCGAGACAGCAATATATACACATTATCCTCTGATAAACAATTGAAGAAACAGTGCAAGAGAGAAAGAGTCCGAGGTATTTCGCATTCGAGCCAAT
Seq A exon
GTACGTAATTGCCGCAAACGATCCCATAAGCTTCGAATATTCCCAATCCACAATTAAAGATTAAATTCAATTAAAATGAAAATAAGGAGGGAATTTTAAAAGTTTTTTCAACTTTATTCGTGGCTTATCATATTTTTGGATAGTTCAACTGTTCAAGTTCCTTTACTTTTTAGTCCGACTTGCTAATATAAAGTGAAAATGTTGCTTTATATAAACTTTTTTTTTTTTTAAATTTGTTGAATAACTCAACGGTGTTTAAGAGTTTAATACTGATAGCATGTAAAAGGAAAGTGCTTTAGGAGAAAGAAATTAAGTGTTGTTATGTACAAAATTTTAAGGAATTTTTGTTTGTCTGGAGTCACCAACTAATTTATGCTTTAATTTTATATTTAATGGAATTCGTACAACAGAGAAATAGAAAAATAAGGTTCCTGGCATTCACTGTGTTTTGAAAAGTATTTTCTGTTAGGTTTTCATCCTTTGATTAAAAGTAGGGAATGTGAGAAGCTTGTAGGGTAAAGATAGTCGCCATCAGCGTCGACTATATAGTTTTCCCCTTTCCGATTCAG
Seq C2 exon
GGTCAGAGCGACAGGGACAAGGATGGGCCTGCTCCTGCCCATAATCCTGGCACTGGCCATCGGATCCTCGGCCGCCGGCATATCCTCCAACGATCCCTGCTACTTCGAGGGCAAGCCGCGCAAGTGCCTGCCAAGCTTTGTGAATGCCGCCTATGGGAATCCCGTTCAGGCATCCAGCGTTTGTGGCGCCCAACAGCCGGAGCGTTACTGCGAACTGTTGCGCGACGGAAATGCCGGCGAGTGTCGTTCATGCGAACAGCAGCGGTACGGTCCGGCGGCATTAACCGATCTAAATAATCCCAGTAATGTGACCTGCTGGCGATCGGGTGCCGTTAATGTGCCCCACGATCCGGACAGTGCGCCGCCGGATAATGTGACCCTAACCTTGTCGCTGGGCAAGAAGTACGAGCTGACCTATATATCGTTGTCATTTTGTCCCCGCTCGCCGCGTCCCGATTCGCTGGCCATATTCAAGAGCTCGGATTTTGGACAGACCTGGCAACCCTTCCAGTTCTATAGCTCACAGTGTCAAAAGTTCTATGGACGACCGGATCGCGCTAAGATCTCCAAGTTTAATGAGCAGGAGGCCAGATGCATCAATTCGCAACATGACACGGGCGGAGCTGCTCAGCGATTTGCCTTCAATACATTGGAGGGTCGTCCGTCGGCCAATGATCTGGATTCCTCGCTGGTCCTGCAGGATTGGGTGACGGCCACGGATATAAGAGTTGTATTCCATCGCCTTGAATTGCCACCACAATTGTTGAAGGTGAAAAATGCAAATGCCTTTAGCGATGAGATGGGCGGCAGTCGCGAGGAGGATGAGGATGATGATGCGGATCTGGAACTGGATGGCGAGCAGGATGAGTACGACTACAATCTGCAGGACAACGACAGTGCCGATGCTGGGTACGATGAGTACGAGGAGCCCAAGAAGCATTTGGAACTGGATGATGATCATCTGCATTTGGACTATGCCAGTGATGGTGAATCGGTTGTAAAGAGGCAGGGCAAGCACAAGGGTAGCGCCTATGAGAAGCACTACCAGAGCAAACTGGCGGCCACCACGCCCCCACAACAGCCGCCCAAGGTGACGCCACCTGGCAAGGTCACGCCCCCTAGCACAGCTGCCCCTTCTGCCGCTGCCTCCGCGGTGACCTTGCCCATTTCGCAGCATTACGCCGTATCGGATTTTGCCGTCGGCGGACGATGCAAGTGCAATGGTCACGCCTCCGAGTGTGTGGCCACCGTCAGTTCGGGATCAGGAACGGCACTTTCGGATCAGGACGATGGCCAGGACGAGGACACGCCGTCCGCCCCCTCGCTGGCCAACCACTTTGGTCGCAGTACCCAGATGAGCGCCAAACTGACCATGACCTGCGCCTGCAAGCACAACACCGCCGGACCGGAATGCGAACGCTGCAAACCCTTCTACTTCGATCGACCCTGGGGCAGGGCCACCGACAATGATGCCAACGAATGCAAAA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0015774:FBtr0073940:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.357
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0005512=Laminin_N=WD(100=44.5),PF0005319=Laminin_EGF=WD(100=18.3)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0073757
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0291226, FBpp0291227, FBpp0291228, FBpp0293414, FBpp0293415, FBpp0303986
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:
CGTCGCCGTGTCTTGTTTTTG
R:
CTGGATGCCTGAACGGGATTC
Band lengths:
345-914
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)