DmeINT0036257 @ dm6
Intron Retention
Gene
FBgn0016754 | sba
Description
The gene six-banded is referred to in FlyBase by the symbol Dmelsba (CG13598, FBgn0016754). It is a protein_coding_gene from Dmel. It has 8 annotated transcripts and 8 polypeptides (6 unique). Gene sequence location is 3R:23894174..23922973. Its molecular function is described by: chromatin binding; DNA binding. The biological processes in which it is involved are not known. 14 alleles are reported. The phenotype of these alleles manifest in: wing vein. The phenotypic class of alleles includes: viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of low expression. Peak expression observed within 12-24 hour embryonic stages, during late pupal stages.
Coordinates
chr3R:23894174-23897191:-
Coord C1 exon
chr3R:23896209-23897191
Coord A exon
chr3R:23895498-23896208
Coord C2 exon
chr3R:23894174-23895497
Length
711 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGC
5' ss Score
5.89
3' ss Seq
CTCACCATGCGACCACAAAGGAG
3' ss Score
-0.3
Exon sequences
Seq C1 exon
GCATTTGTAAGAACAATGTGTTTACCCAGCCCAGTGGGATCTACAAGCATTCGGAGCCAAAGATCAGACGCATCCACATCACCTCACAGACGTCGGCGGAGAACGGAATTAGCCTGATGCAGGGACAAGGTATGCGCCTGGCGACATCTAACACAAACTCCACATCTGCATCCATGTCTATAACATCGTCATCGTCGGCACCACTAACCACAACTGCTCTGGCTGGTCAACGCCAGCTTATGCACCGCCAGCAGGCCGTGCACCATCACATCCCAAACATCTCCAATAGCCATCCAAACACCTTCCTTCATAGCCACAAAGTAGTTAACTTTGACTATCAGGGTAAGGACCCATCGCTGACCAGCACTAATTGCATCCACACGCTAACCCACCAACACAACACCACCCGTTTGGCGACTGCATGATCGCCTGCACCACCTACAGCACATGTACCTGCACCTTTGTTTAGTTTAGAATCTCTACCCTTCGTCTGTACTTCGCTGGGTGCTGGGATCACCATTGCCCCCGAGTAACCAAATTCGTAGTCCTAGTTTCTATGAGTGTGTGTGTGTGCCTTTCGTAGAGTCGCCCACCACAACGCAGCTGCTTTCATCAGTTCCAACCGCTCAACCAACAGTCGAGAAGACGACGGTCAGGACGCCCACGAAACGTTCGCGCCGACCGCAACGAGGGGCAGCGCGTGCGGCGCCCTCGGCGTCTGATAAAAGTTTCCCGCTGCCACCACGATCCTTTGCCATTGGGGAACTGATATGGGGTCCAGCTCGGGGCCATCCCGCCTGGCCCGGAAAGATTGTCAAGATGCCAGACGGAGTGTGCACGCCGTCGCAGCAATTCGACCACGTCTGGGTTCAGTGGTTCGGCGGCGGCGGTCGTTCGACCTCCGAGCTAATTCCGGTCAACTCATTGCAGAGTCTCTCCGAGGGTCTGGAAGCACATCACAAGGCCCAGAAGGATACGAGAAA
Seq A exon
GTGAGCATCGACTAAGGGTGGGAATTTCTGGAAGAGATCAGGAGGGGAAAATATTTATTCAAGTTCATATTTAAAACAGGCAGCATTTCAGGAAACCTTCGGCTTTAGGTGAACTCCAGACCAGCTCTGTAGTTAGTTTTTGTACGATTTTGAAAAATATTTGTTGAATTTAAATTTATAAAATTTTCCTATCTTGAAGTAATGCGTATTTATCTTAACTTTGTAGTTTATTCTTGCATATTGTATGAAAGCAAACGTTACAATTTTTGTTTTGTTTATTTTTGTATACAAAATATTTTCATTTCTTCTAGATAACTTTTTAGTTTATTTTTTGCAGTCTTTATTAAGCCTTACAACCGTAGCTACATATATTTAGAAAATTGGACACTTTATATTATTAACTATGCAATTAAGCGATAAATCGGCATTTAAATGCATTATTAATTAGTTTAATCATTGTTTACAATTTGACTTTTAATTTGCTAATTAATATTCTTGTTTCTTTTTTTTTAAATGCGCTGAACCAAATCCAAAAATTAAACCATGCCCCGCCAACCCCAACGTGTATAACTCTGTGTGTGTATGCATAATCATCATCATCGTCATGACCAACAACAACCCCACTCGAAAATGAAAAACCCAAATCCGAACCCAACCTGAAACCAACCAAAAACTCAACCACATATACACACTCACCATGCGACCACAAAG
Seq C2 exon
GAGCCGCAAACTGAACTCGCAGCTCGAGCGGGCCATACAAGAAGCAATGACTGAGTTGGATAACATTTCAGCCTCCTCGACACCCGCAGCCACATCCTCGTCATCCGCAACCATCTCTGCTGTTCCCGCATCAGCAGGACCAGCTGTAATTGGCGGACAACAGCAGTATCAGCAGCAGCAGCAGCAGCAACAGCAGCAGCAATCGCCCTCTTCAACGAACAACAAAATAAATGGACTCGCGCGGAGCAAGCGCCAGGCCAACACAAGTGGGGCCAGCATGGTGCTGACCACCAGTACGGCGGCCACATTGAGTGGCCTCTTCAATCAGCAGCGAGCCAAGCCCATACGCATTGCTCCGGCTCCACCGGTGGCCACAACGGGCACAGGCAACATTGGGACGATAGCAGCAGCTGGAGCTGCAGCAGCTTCAACTGGAACCGGGACAGCGACAACATCGGCCCGTTCCGAGATCCTGAAGCTGGCCAAATGACCAGCGCTGTCGACGTTATCGTCGACAGTGAGCACAGCCAGCTACACCCTCGTTATCGGGCATAAGTAGTGGGCAGCAGGAGGATACATACCGCCAGGCCATATATATAGAGTTATCCATACATATGTGACGATACGAGTATAGAGTTTAGTGTTAGGTGTCAGGCCTCAGCTTTGGAGTTTGTTGTTTTGTATTCTTTGACAGACTCCCCGCTTAGTTGCGTCGCTGGGCGGCGCGCGCCACACTTTCGAAATAGACAATAAAACAGCAAGATGATGTTAATGAAAATCAAGTTACAAAGAGCAGTTCTAACAATTAGCGATAGGTTTTTGGCTTCATAGACAGCGCCTCGGCGCAAATTTGCGTTGTTTTGTATATAGTAAGCACCAAAAGCTACCAAGATGTTTCGTATTAAGTATTTATTTATTGCATATAGATCCTTGGTTTTTATAGGTTTTGTTTTCGTTGCAATTTATAGACCTACCGATTATTTGTATAAATAGGTAACCTAAGCTGATACTTAGCCACTAAGTTTAAAGAACATCCACAACAATTACATTTGCCTTGTCAAGCAAATGATATCAAATCAAAAACAGCTACTGATTTTCATTTATTGTGATTGCACAAATTGTTTTTTAAACTCTAGAAGAACAAATTATTTATGTCAAACACAAAAAGGTAAAAATCATGAGAAAATTAGGAAGGGTGGAAAAAAATTATATTTATAAATTGTTATTATTTATTTAGTTGAAACTATTGTAAAATTATAATTGTAAAACAAAAATGAAATCACACTTAGCGGAAACACACGGAGCAAATAAAAATTTAAAAAAC
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0016754:FBtr0112888:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.822 A=NA C2=0.817
Domain overlap (PFAM):
C1:
PF0085512=PWWP=PU(80.2=57.5)
A:
NA
C2:
PF0085512=PWWP=PD(18.8=11.0)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0303406
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0111801, FBpp0111802, FBpp0300786, FBpp0300787, FBpp0300788, FBpp0307193
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:
TGGCCCGGAAAGATTGTCAAG
R:
GATACTGCTGTTGTCCGCCAA
Band lengths:
355-1066
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)