DmeINT0032376 @ dm6
Intron Retention
Gene
FBgn0001148 | gsb
Description
The gene gooseberry is referred to in FlyBase by the symbol Dmelgsb (CG3388, FBgn0001148). It is a protein_coding_gene from Dmel. It has 2 annotated transcripts and 2 polypeptides (1 unique). Gene sequence location is 2R:25061964..25064643. Its molecular function is described by: RNA polymerase II regulatory region sequence-specific DNA binding. It is involved in the biological process described with 7 unique terms, many of which group under: developmental process; anatomical structure development; multicellular organismal process; regulation of biological process; multicellular organism development. 39 alleles are reported. The phenotypes of these alleles manifest in: adult sense organ; adult procephalic segment; adult thorax; pCC neuron; external sensillum. The phenotypic classes of alleles include: increased mortality; phenotype; increased mortality during development; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of extremely low expression. Peak expression observed within 00-12 hour embryonic stages.
Coordinates
chr2R:25061964-25064643:+
Coord C1 exon
chr2R:25061964-25062202
Coord A exon
chr2R:25062203-25063233
Coord C2 exon
chr2R:25063234-25064643
Length
1031 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
TGTTTCTCTAATTCTTCCAGGAC
3' ss Score
9.9
Exon sequences
Seq C1 exon
CAGTTTCGAGCTGTCAAGCAACCGAGCAGCATCATCATTCACTGCGCACTCGCAACAGCAGATACACACTCCAAAAATAATTTAGAATTCCTAACAGTCGGGCCTCGCGAAGATTAATTTGAAACGTATAAGTAAAAGTGTTAACAAAACTCCGAAGAACTCTCAAAAGGATTACCGCAAGGAAATGGCTGTTTCGGCTCTCAACATGACACCCTACTTTGGCGGATATCCCTTTCAAG
Seq A exon
GTAAGCACCGACAGATAGATACAAGATCACAACGACCATTACCAATTACCACAATTACTGGTACAAAACGCCAGATTCAGACGCAGAAAAGTGCTGGCTCATCATTTGGGGCAGCGCTTTCGCCCGCTGTTTTCAAACGAGGGATCATTACCCGTTCGGCAGCATGATCAGCTTTCTGACTTATTGATTGTAATCGGCAACTAGCCCGGACAGGCAATGGCCATACCCAGACCCAGTGAAAAGCCAACCTCTTCGAACCCCAGCTTAAGGTGCGGACTTTGCAGACTTTTTGGCGCGACCGTCTTGCCAGCTCATGTCTCGACTCATGCCACGGCGGCGTCGTGTCGCTGGGCTTTGATCTTGAATCGACTCAGTGTCTGTGTTGGAGCTCGGGGTCTTGTGTATCACGTAGCTCAGTAACGTCAGCGCCCCAAACATCAGACCCTGCACAGGGACCGGGCTTTCATTTCTCTTTACGGCTGTTTTGGGGCCGCCTTTTCATATACACACACTTGTATTAGCCGGCGCAGCTGGGCATCTGCTGCTCTTATGGATTATTAGTTTGATTTGATTGCAAAAGCCGGCCCGGGATGCAGCTATGTTCGCAGCCGCGTCCCCTGTCGAGATTGGTATTTTTCCCCACCACCGCATACCATTCGTCTGCAAGAGGCTTACTATTTTCTCAAAAAGGCCCACGCAAATGACCAATTTGCGTTTTGTTATGTCTACAAATGGCTATGGTATCGTTTGTGCCAATCTTCAACAAAAGATCGTGCGTATTGATCCTGCGGCTTATCCTGATTAGTGCAGTTCAGTTAGTAAGCAATTGAAGTGGTCAATGCCGTCTAACTAGATTACTTTCTTTCGCTCAATGGAGCAAGGAAAAAAGTTAATTTAAATATCGTTCCGAAAACAAGACCACACAACTAACGTACTTAAGATATTGTAATGGGATCAGACTTCCATGGACGTACTTACGAACAAATGCTGACTTGCAAGTGTATTCATGCCTGTTTCTCTAATTCTTCCAG
Seq C2 exon
GACAAGGTCGTGTCAACCAGTTGGGTGGCGTCTTCATCAACGGCCGTCCGTTGCCCAATCACATCCGTCGCCAAATCGTGGAGATGGCAGCAGCTGGAGTCCGTCCCTGTGTCATCTCCCGCCAGCTGCGCGTCTCTCATGGCTGCGTCTCAAAGATTCTAAACCGCTTCCAGGAGACTGGCTCCATTCGGCCCGGAGTAATCGGTGGCAGCAAGCCCCGTGTAGCCACGCCAGACATTGAGTCCAGAATCGAGGAACTTAAACAGTCGCAGCCCGGTATTTTTAGTTGGGAAATCCGCGCCAAGCTAATCGAAGCGGGAGTCTGCGACAAGCAAAATGCTCCGTCGGTGAGCTCTATTTCGCGTCTTCTGCGAGGATCCTCCGGATCAGGGACCTCCCACAGCATCGACGGCATCCTCGGCGGAGGCGCTGGTTCTGTGGGAAGCGAGGATGAGAGCGAGGACGATGCCGAGCCCAGTGTGCAGTTAAAAAGGAAACAAAGGCGTTCCCGGACGACATTCTCCAACGACCAGATCGACGCCCTAGAGCGCATCTTCGCCCGTACACAGTACCCCGATGTCTACACCCGGGAGGAGTTGGCCCAGAGCACGGGATTGACCGAGGCCCGTGTCCAAGTTTGGTTCTCTAATCGCCGTGCTCGTCTGCGCAAGCAACTGAACACCCAGCAGGTGCCTAGCTTTGCTCCCACATCTACTTCTTTTGGCGCAACTCCCACTACCAGTGCCGCCCCTGCTCCAAACATGGGAATGAGCCTTTACAGTTCACAGAGCTGGCCATCATCCGGAGCCTATGAAAATCATGCTGCCTATGGTGGATCGGTTGCATCCATGTCCCCCGCCAGCAGCACCTCGGGTACCAGCTCTGCCGCCCACAGTCCCGTACAGACGCAAGCGCAGCAGCCAGGAACTGGAAGCGAGTTTATGACCTCCACTTACGGCGTGGGATCGAGCAATGCTACTTACCCATCGGCTGCCTATTCAATGCCGCAGACTCCTGCTACATCCGCGGAGCAGCTGAGATCCCAGTTTGCATCTGCCGCCGCTTCGGGCTCTCACCACCCCTCCACGTGGGACAGCTACAACTTTGCGGGTTCCTTTTTCCCTCCCGCTTCTGCCGCAGGCAACCATATTAGCGGCTACCATCATCAGGTTGATCAGAAGAGCTCAATGATGACCACTGCACCAACCTATCCATACTTTGGATTTTGAGACGATCCCTGCTTGTTCCTAATCTTGTGGGTCGTTTGAAAACTTTAACAGTACTTTAATGTTGCTACTCGTATAGACCTACATTTAACACCCCTAAGACTGTTTAAATTAGTACTTTAATACAAATGTTAGTTTTAGGTTAAGGAGCAATTATCAAAACAATAAAAGAAAACATTTAAAT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0001148:FBtr0072444:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (disopred):
C1=1.000 A=NA C2=0.592
Domain overlap (PFAM):
C1:
PF0029213=PAX=PU(0.1=0.0)
A:
NA
C2:
PF0029213=PAX=WD(100=30.5),PF0004624=Homeobox=WD(100=13.9)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0072349
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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:
CATGACACCCTACTTTGGCGG
R:
CTCCCGCTTCGATTAGCTTGG
Band lengths:
356-1387
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)