DmeINT0037080 @ dm6
Intron Retention
Gene
FBgn0035676 | ssp6
Description
The gene short spindle 6 is referred to in FlyBase by the symbol Dmelssp6 (CG6619, FBgn0035676). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (1 unique). Gene sequence location is 3L:6076722..6082491. Its molecular function is unknown. The biological processes in which it is involved are not known. 5 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: partially lethal - majority die; some die during pupal stage; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of extremely low expression. Peak expression observed within 06-18 hour embryonic stages, at stages throughout the pupal period.
Coordinates
chr3L:6076722-6079281:+
Coord C1 exon
chr3L:6076722-6077345
Coord A exon
chr3L:6077346-6078918
Coord C2 exon
chr3L:6078919-6079281
Length
1573 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
AATATTTAATGACATTCCAGTTA
3' ss Score
1.88
Exon sequences
Seq C1 exon
ACGGAAGTGGAACAAACCAAGCGGAAACAGACTCACGCGACAACAAAACCGAACCGAACTCGAATATGGAAAACTTTTACCCAGAACCGATATAGCACTGATAAACGCAACTCGGAGTGAACTTTATGAATGGCCATGACTAATTGCAGTCATCTAGCAGCAGCCACAGTCGATGTGTGAACTTCAGTGGTGAAGGTTGTCCGGTTTTGCAGCGAAAGATACCCGTGTTTCGGTATCTGTATCTGTCGGTGTCTCATTTGAGCGGCTCGAATGATCCGCCTGTAATTATGACTGCGTGAAGAAATCAATAAGTGGAGGATGGCCAGCAAGCCCATGAGCACCAGCTGCCAAAGCATTGCGACGGCGGCCAGCAGTGCGGCCACCACGGCGGCAGCGGTGTCCATCTCGGCCTCCAATGCCACCTCTGTAGGCTCCCTCATCGCCGCCGCCTGCCAGCAGGAGCAGCCACATCCCCACCAGCACTATTCCCAGTCCCAGCAGCAACACCTCTATCATCAGAGCCATCAGCAAGCGTCGCACTATGTCAATGGCACCGGCAGCTTGGGCAGGCTCAAGTTCCACAAGAGTCTCGATGCCAGCGACGAGGAAATCGAGTATGCGCAG
Seq A exon
GTATGTCCAAGTGGCCAAGTATCCAACTGCTAGTCGGAATCGTCTCCAACTGAATTCAATTGTGCCCCACACTGAGTCATAATAATGCGACAAGGTCCTGCACTGCTGGCTCAATTGAATTTGTCTTGTGGGTGGTGGCGGTGTTGGGTGGTGTGTGATGGATGGTGGTTGCTTGCTGCCTTGTTGAGTGGGTGTACTTGGGGGTGGTTTGCGCAACCTAGCTCCCATCCCAGTGCATTTGCTGCCCCCACAGCTGTTTAACCCACCAGCCGGGTCGTTATGCATAGTTTACGCTTCGCCAGGCAACCTCAACAGCCGCCAACAACCGCCGTCGTCGATCAAGTGTTAATAATTCAATGCCCCGGAAATAGTCATATATTGAAATATATCGTACACCCTGCGAGCAGCTTAGTCCCTGCAAGGGCCTTGACTTTGGCCAAGGCAATTTGAAAAATTAACCAGTTGGATTAATTTATGGGTCACTAAATGAAAGGGGCATGTTTGCGAGCATGCCATATTTACAGCACCATTAATGGGGAGCTCGGTCAAAATTTCTACTAAAGTCACGATATGAGCCACAATATAAAAATGAATGCAGTTAATACAGCTTTAATTTGAGGACTACACCTAAACACAGTTTTTACTAGAATTAATGGAATTAAACTTACATACTCAAATGAATTAAACCGTTCATAAGGCAGAAACGATGAATTCGTGCACCATTTTTTTTATAGTTTTCTAACTCATTTTCTCCGCGTTTTCTTTTTTAATGAAAATCTTTACAATTTCATTTAAAACGGGCACTGTATTTCTGTACATAATGCCATACAATTTGCTCTTCCTTGCCGATGGCATTATAGTCGGCGGGAGGTCTGTTCTAAAGCCTTTCAAGCCAGTTATTACGCCCGCACAAAAAAGCGTTAATGAAAGAACTGTGCTGTGTCTCTATACTTAGCATGTTGTATCTAAAAATAGGTGTCATCGATATAAATATAAAAATATTATTAGTACACTTGTTTATACCATGAACTTTTCCGAAACTTTAAGCTTGACTATCTTACAAATATTGTTTTTTGTTTTATTCTACTACCAACTTGTTAATCCGTGGAAATGGCTTGCATGGTATTATTTTGTCCGTACCTGTATTCTGGGTTGGTTTGCTTTTCCCTATCTAACCCGCTTTCCTTTCGGGGGGGCAGTGAAAGTGTTGCCTGCTGGGGGCTTCATCCTGTATTCATAGAAATGCTTTCAATAAAAGCAGGAAGAACAGTAGGGACGAAGGAATGGGCTTGGCAAACATCATTTTGATGGTTTGCACCACCACACCTGGCGGCTATTTGGTGTGCCACATTGCCTAGACGTGCAAATACCCGGAAGTGCCAACGATAGTTTAGCATATAAGCTTTTCACTTTCACCGCAAATCAACACATTCCTTTCACAGATAGAGAGCACAGCTCTCCAATGGCCAATGTGGTTTGAATTGCTATAGAGAATTGCGTTCTTGCTAAAGGAATTCCATATTATTGTACAATATTACATATTATGCACGTTTAATATTTAATGACATTCCAG
Seq C2 exon
TTATCCCGTTCTACCCATATCCTTGGGCGCCACAAATCCGAGCGATATCTGGCCTCCAATCCGGACGAGGACCGAAGACGTCGCACCATAATCGTTGAGAAAAAGAACAACTCGTATGGATTCACGCTGCAGAGCTACGGGATCCACTACAAACGGGATGAGGAGCTGGAAATGATCACATACGTGGACTACGTGGAGTACGGAGGTCCGGCCTATCGAGCTGGCATGCGTGAGGGAGACGTAATCCTCTCCATTAACGGAAAAGATATGGAGAAGGCGGACCACAAGACCATCGTCGAGTTCATCAAGCAATGCGACACCAGGATGAGAATGGTAGTGCTTTTCGAGGACTGTGTGAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0035676:FBtr0077049:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.412 A=NA C2=0.190
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0059519=PDZ=WD(100=71.1)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0076757
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0311663
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:
GCAGGCTCAAGTTCCACAAGA
R:
TGTGGTCCGCCTTCTCCATAT
Band lengths:
345-1918
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)