DmeINT0027105 @ dm6
Intron Retention
Gene
FBgn0052654 | Sec16
Description
The gene Secretory 16 is referred to in FlyBase by the symbol DmelSec16 (CG32654, FBgn0052654). It is a protein_coding_gene from Dmel. It has 7 annotated transcripts and 7 polypeptides (6 unique). Gene sequence location is X:12596047..12609910. Its molecular function is described by: Ras GTPase binding. It is involved in the biological process described with 10 unique terms, many of which group under: endomembrane system organization; response to starvation; endoplasmic reticulum organization; stress granule assembly; response to nutrient levels. 8 alleles are reported. No phenotypic data is available. The phenotypic class of alleles includes: viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed within 00-06 hour embryonic stages.
Coordinates
chrX:12604861-12607707:+
Coord C1 exon
chrX:12604861-12605388
Coord A exon
chrX:12605389-12605802
Coord C2 exon
chrX:12605803-12607707
Length
414 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
TCTATCCAAATGGAATGCAGCCC
3' ss Score
1.54
Exon sequences
Seq C1 exon
CAGCCCCAACAAGAGCAGCTGCAACAACTGCAGCAGAATCAGCAAGTCCAGCAGGAGCAAAACGACATCGATCAGCAGTTTGCAGAGGTGAACAAGCAATTCAGGGAGCTAAACATGCAATACGAGAGCAACAGCAACATGGAGAATACGCTGCAGCCGCAGTTGCCACCGGTGGATCAACAGCCGCCGCAACAGCAGCAACAAGTTTTATCGGAATCGTACCAACAGCCAACACAACAATATTATGAGCCACCACCTCAAGCGCCAACCGAATCCGATCCCTATGGACAGGGCCAACCGTCCTATTATGATCCCAATGCGGGGCAGCTTCATTACGATCCAAATGCTGCACAGCATCAATACGACCAGCAGCAACCTCAACCACAGCCGACTCCCAGCTATGGCCAAATAGAGCCAGGAACTGAGGCCTACCAACCTGGACAAGCAACAGCAGATCCAGCTGCGGTTCCCTCTGGCTACGGATACGATTACTGGTCGGGCACACAGCAGCCACCTTATGGTGACGAG
Seq A exon
GTAAGTGCTGGTTAGCTATAGTCAGCCGTCCTTAAACCCTCTGTATTTCCATTTGATGAACTCATTTTTTTGATAAAGCTCCAAAGTTCGTTTAAAAATTGTGGTTTTCCGTAGTCGCTTTAAAGAAATTTCAGCTCCCTTTTATAGGATATAAAATAAGCATACTCTTGAATTGCTATACAGAGGGTTAATTTGTTGCTTATTTTACCTTTTTAGTTCGTTTTAAGTTGATCAATGTATGTTATGCTTTAGTTTTGTATTTTATGTAATTCTGTTTACGCCTTAAGTTTTGATCTGTCTTGAACTTGTGTTATAGCCATAGAAGTAGGACTCGCCAAATTGCTAACATGTTTCTAATCACATTGCACACACAAAACGAAAATATAAACATGCCTCTATCCAAATGGAATGCAG
Seq C2 exon
CCCAATGAGAATCAAGCTGCACTAAAGGATGAAGAGGAGGAGGATGAGGAGCAGGATGAACAGCAGATATTGCAGTACGCTAAACAGCAGATTTTGCAGCAAACCAAGCAGCAGCAGCTGCAGCAGGAGCAACATACTCGCAGCAATGGCGCCGCCAGCATCAACAATCGCTTCAAATCGAACGCTCTGAAGCAGGAACGCAGCAGCGGCTCATTGCGGAAAAGGCAAGAGGCATCACGAACAGCAACAATAGCAGCGGCAGCAGCAGCTATTGCTCAGATAACACCGGCAACAGTTGCAGCGGCAGCGACGCCACCAGCAGCATCGGCAAAGGCATTCAATTTGAATGATGTAAGTAGCTTTTCCAGCACAAATAAACGACATCAAGCTACCAGCAGCAGCAACAATCGCAGCAGCAGCAACCAAGCAGCAGCAGCAGCAGCAGCAACAAAAGCTGCAGCAATAGCAACAGTACCTGCTGCCCCTAATCAATTGCTAAGTTGTAGAAAGTCTAACAGCCAGAATAGTCCATACTTAGCCACGCCAAAAACGCTTACCACGCCCACACGTTTTATTGCCGCTAAAGCAGCCACTGTTACAGCCACGCCCACAGCGCCAGCCACTTCGACGACAACGTCGACAACCATAGGTGCTAGAGGATCATCTACCAAACGCGTTTACTTTAATCTTCCGTCGACCATTGCTGAATCGGAGCAAGAGTTCGAACATGAGCTGGATTATGATGAGGAGATGGAGGAGGAGAACAGTATGGCTCTGGCGCAAGCTAAACCAAACGTTCATCTAGCGCGAAAGCCACATATTGTCTTTAATGGAACGTATCCCATTGATATGCCACTGACCCAGGGGCAGAGTCAACTCAAAAGCAACTCGTATGATCCGGAGGCCAATGCAGATCGTGGGGATCTACAGCGCTATAGGAACTACATGCTCCACGATTATGTTATAGATGAGGATGCCGAGGGCGAGGAGCAGGCCGAAGAAGAGGGCGAGGAGGATGAGTATGGAGATGGTGATGAGGATTTATTCCCCTATGCCGACGACGATGAGAGCTTCGATGATGGCGATTACTATACGCATCAACTGCTCAATAAGTATGGGATTATACCAAGCGGTGAGAAACAGAGAGTCGAGAGAACACCGGCATCCGTGGAGGCAGCTACCTCCGCGGCCCAGCCACAGCACGTGTGGTCCATGAAGGAGCTGATAGCCAATCCAGCCATACCACTTAACTACAAGAAAATGTGCTCCGAAGTGGAGCAGAGCCTCAGTCGATTCGAGAATTATTTGGACAGCAAAAAGGAGCAACAGGTGCCACCGGGAGCCGCAGTGCGCACCTTCGACATCGATGCACCCACTCGAAGAGGCCACCGAAGCAGCACATCCACAAATGCTGGCTTGGATCTTAGATCTAAGAAGAAATTGTAAACAAACTGACTGCAGTTTGCTGTTTTAGACTTAGTAATACCCACAAATGATCAGTCAGTATTTACAAATTCAATGAGTTAGGTAACAAGAAAATAAGGATGAGCAAGTGCATCGCTGCTTTTTTGGGAGCTTTCTGTACTGTACCTGGAGCTTGTCTTAGCCTGTTAGCTTGTAAATCTATAACTAGTCTTAATGCGTCCCTAAGCAATATGTTATCACTAAGCCTTATATACGATAATTGTGAGCCAGATTTTTTGACTGCGCCAGTTACTTTGAAACGTTTCCGTTGTTCATTCGATTTAACTAACCCATAACTACTCTGTTACTAACCAACCCAAAACACTCTTACCTATAATCTATGACTTATGAATAATTCGTTTGCATCACGCAGAAGACTAATTCGTTGCCATTTCTTAACTCCAACCTCAATTTTGCAATCCGCACAACAGCTGCAGCAAC
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0052654:FBtr0113444:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.959 A=NA C2=0.787
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0309104
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0112356, FBpp0112357, FBpp0301987, FBpp0309103, FBpp0309105
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:
ACCAACCTGGACAAGCAACAG
R:
TTGTTGCTGTTCGTGATGCCT
Band lengths:
348-762
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)