DmeINT0002930 @ dm6
Intron Retention
Gene
FBgn0033473 | CG12128
Description
This gene is referred to in FlyBase by the symbol DmelCG12128 (FBgn0033473). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 2R:10026839..10030668. Its molecular function is described by: . It is involved in the biological process described with: . 9 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 moderately high expression to a trough of low expression. Peak expression observed within 00-12 hour embryonic stages, in adult female stages.
Coordinates
chr2R:10026839-10028498:+
Coord C1 exon
chr2R:10026839-10027643
Coord A exon
chr2R:10027644-10027707
Coord C2 exon
chr2R:10027708-10028498
Length
64 bp
Sequences
Splice sites
5' ss Seq
GTGGTAGGC
5' ss Score
5.59
3' ss Seq
TGAACTATTCGTCCTAACAGAGA
3' ss Score
7.51
Exon sequences
Seq C1 exon
TTATGTTCAGACCACATACTGTCCACCGAGGTTGCACGTGCGTATTTTGTTTGCAACAGTTTCAATCGAGTAAACGAATTGTTGATGAAAACGATGCTCGCCGCCCCCACAGCCAGCAGCAATGGGAGGCCTATTGGGCCCCACAAGTCCTGGAAGAAGGTGAACGAGGAGCGGAAAGCGTTGAAGCGGCAGCGCAAGCAGGACAAGCTGCTCAAGGAGCTGCAGCAAGCCAAAGAGGCAGAATCACAGGCGGGAAAGGCAGCCAATGAGGTGCAGGCTAAGGATAAGCCTAATCCGTCCACGCTGAGCATAGCTGTTCCCGGTTCAATTCTCGAGAATGCCCAATCCAACGAGCTGCGGGCCTACGTGGCCGGTCAAATAGCCCGGGCCGCCTGCATCTTTCGGGTGAACGAGGTAATCGTCTTCGACGACGTGGGTATAGCCACCGCCCGGGAAACAAAGCGTAGTTACGAGGCAGATGGGGAAGGCAGCAGCACTGGCACTGTGCGCAGCAGCTCATTACAACTGGCACGCATATTGCAGTATCTGGAATGCCCGCAGTATCTCCGAAAATACTTCTTCCCGCTGCACAAAGACCTTAAGTACTCTGGCTTGCTGAATCCATTGGACACACCGCACCATCTCCGTCAACAGAGCAAATTCAGGTATCGTGAGGGCGTCATTTGCGACAAGAAGGCCAAGGAGGGACACAGCTACGCCAACGTGGGGCTGCTTAACGACGTTTTGGTTGACAAGGCAATAGAACCAGGCGTCAGAGTAACTGTAAAAATGGAACCTCAAAGTG
Seq A exon
GTAGGCATTTAAATCGAACATTTGTGCTCCCAGTGCCGAACTAATGAACTATTCGTCCTAACAG
Seq C2 exon
AGAGCTGTAGAAAGCAGCGGGGAACACTAGTTAGCCCGGATGAACCACGTCGGGAAACAGGTGTTTATTGGGGCTACCAGGTGCGCATCGCACACTCCATGTCTGAGATTTTTACCAAATCACCCTACGCAACCGGCTACGATGTTACGGTGGGTACCTCGGATCGCGGAACCAACGTACATGAGGTGCCCAACCGATCATATAACTTTAATCACATGCTCATTGTATTTGGCGGACTGCAAGGCTTGGAATCTGCCTTGGCCAACGACGAGAAACTGACCGTAGATGATCCTGAGCTGCTGTTCGACCACTATGTAAATGTTTTACCACGCCAAGGATCTCGAACCATTCGCACCGAGGAAGCGCTGTTGATTGCTTTAGCGGCTCTCCAGGAGAAACTGCAACCGCAAGTGGCTGATGTGGAGATCGATTTGACTGATCTGCTACCTAAAAGTGAGGATTCAGGCATTGCAGTACGGCGAGATGTTTTAGTTAGCAAAAAGCAAAAGAAAAGGAAGCAAGTAGAGGATACTCCTGATGAAACAGTCGTTGATGAACCTTCATTTTCAAAACCATTGCCGAAAGTGGCTCGACTGACGGCCAATCCTTTTGCCGATTCCTCCGAGGAATTAGCGAAAAACACCCCAGCACAAGACGATTTTGAAGTGGTTTCATCCACCACCGTTTCTGGAACAAGCCACTCGTGTGCAGATGACGACTTAAGTCGGTTCGATTAATGGGAATAGTTGGAATTTTATTTTTGTAAATATACAGATCCGTATGTGTTGCTT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0033473:FBtr0088393:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.412 A=NA C2=0.394
Domain overlap (PFAM):
C1:
PF0259812=Methyltrn_RNA_3=PU(56.2=69.7)
A:
NA
C2:
PF0259812=Methyltrn_RNA_3=PD(43.5=52.8)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0087481
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0087482
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:
GGCTGCTTAACGACGTTTTGG
R:
CTGTTTCCCGACGTGGTTCAT
Band lengths:
138-202
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)