DmeINT0025701 @ dm6
Intron Retention
Gene
FBgn0020620 | RN-tre
Description
The gene Related to the N terminus of tre oncogene is referred to in FlyBase by the symbol DmelRN-tre (CG8085, FBgn0020620). It is a protein_coding_gene from Dmel. It has 6 annotated transcripts and 6 polypeptides (5 unique). Gene sequence location is 2R:13984815..13990707. Its molecular function is described by: Rab GTPase binding; GTPase activator activity. It is involved in the biological process described with: activation of GTPase activity; intracellular protein transport; regulation of GTPase activity. 11 alleles are reported. The phenotypes of these alleles manifest in: organism; multi-tissue structure; head segment; circulatory system; female germline cyst. The phenotypic classes of alleles include: melanotic mass phenotype; planar polarity defective; cell migration defective; neuroanatomy defective; 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 00-18 hour embryonic stages, in adult female stages.
Coordinates
chr2R:13986426-13988437:-
Coord C1 exon
chr2R:13988373-13988437
Coord A exon
chr2R:13987472-13988372
Coord C2 exon
chr2R:13986426-13987471
Length
901 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
TTCTGTAATTCTGTTCCTAGGTG
3' ss Score
9.65
Exon sequences
Seq C1 exon
ACAAGAACAAAACGCGATCGACGTTCAGTCCACAGTGTCCTACGAGACTTCGGAGTGCGCAACGG
Seq A exon
GTGAGTCATGCGTCACACACAAGTCCTTACACTGTTTATCTACTAATCCTAATGCTTGCTTTAAACAATCCACTTACCCCACTTGCTGACTGTAACTATAATCTGCAATAATAATTGAAAATTTATTTCTTATTTTGTATTGTGTGGTGCAAGTTTATCACAAATTGTATGTATATATATCATGTATGTATGTATATGTAAACCGAAACACGAGCAGTTCCTCAAATCGAACTTGAATTGGTGTTGCCCTAGACTTAATCCTATGTACAAAGTCCTGTTTAGTTCTAGACTATGATATATGGCATATGTATTATGTTTGATTTGAGTAGCGATGTATAGTTTTCCTTTTGAGTATACGTTAAGATCGTAGCCACTTTCAGCGAGTCATCGTTGGCAGTCCAACCCAAATGCGTCACCATCTCGCTGGCCGAAGCATTAAACTAATTGAATAATATGCTAATATTGACCTTTTGCACGTTGGAGGGAACTAAGAAGGGAATTCCTATTCCTATTTGTGTAATTTGATGGATGGCTCGAAACAGTGGGACGAGTTTAAGTGGTTCTGGATGGAGTACCAAGTTTTAGACGTAGCGGATCTAATGGGCACTAATTCTAACTGTATATGTAAATTATTAGCATTTAAGGGCCAAATAACCAAGGCAGCCACAAAAACCAGTTCATGCTTATTAAATACGCCCCTCGACGTTCATGTTATCGGATGATCCATTTTGTAACCATTGTCTAACATTGTCCGCTGCGTGTACATATATATCCGTTTCGATCACAAGCCACCGCTTCTGCGTCTTGCCGGCAATCGGAGCTGCAAAAAAAAAAAAAAAAAAAGAAAACTCGAAATCAGATCTGACCTAATTTGCAATCGCTTCTGTAATTCTGTTCCTAG
Seq C2 exon
GTGATGGATACTCAATGAAAACGTTTGAGAGTATCACTAGCTTAGCCACCTCGCCGGCGAATAGCAGCTACTCGCTGTACAGCAATGGATTTGTGGTGACCACTATCGATAGTGAACAAGATCCCGCCCGCAGCCAGAGTATCCACAATCTCAGCTACCTGCAGACGCATCCAGCTCTGCCGCCCAACGGGCTGCAGCATATGCGGCACAGCTTTAGCAGCGATAGCGACAGTCGCAATCGCATCGATCTGGATCAGGCACTGGAAGTGCTCCAGCGACAGCAGCTGCCCCTCCATCCGAAGACTCCCAGCAGCCAGGTGGTGTATATCGTGCAAAATGGAGGCGGAGGCGGCAGGTATATGGACGGGCATCGGGATGCTGCGGATGATGATGACGATGATGCGCTGAGCGTGGAGAACACACGCCTTTAATCTTAGTTGATTCGTATTTCGTATTCTTTCTTTATGTAGTTAATGTTTGTTTTGCCCACTTGGTTTGTAAAACGCATATGCCAATAACGAATTCCTTACCCCCCCCCCCCCCTCAAAAATCCCCTTAAACATTCGGTAGTAATATCCACATGTACTTAGCTTTAATTTTTGTATTGTCGAACCGACAGAAACCTGAAATTGTTATTCATTTGCTAGCATTCATCGATGTGTGTATTTAGTGTTTCTTCCACACTCTTTCTTTTCCCCTCGCTCTCCGATATTATCCAACCGAGAGTCTCAACTTAATATTCCAAATACTTATAACTCCTAAGACTCCAACTATTCCGTTTGAAACTACGTACAACGATTAATATTTATTGCTAACCGCCTAACTTCTTACCCACAATTCCACAATACCTACTAGCATAAACCAACTGATTAGGTAACTTAAGCTTTGCTCTTGCATTTACTTTATATTTGCATTACAAACAAAACTCAACTTTTAGTTTATGTTAAAGCCAAAATTGTAGCTGTAATCTAATTGATTAGCCAATAATTATATATGATTATACATATAGCGAAACGTACCACACAAATAAATATGATTTTGTACTG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0020620:FBtr0087605:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.330 A=NA C2=0.720
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
FBpp0086730
Main Skipping Isoform:
FBpp0086731
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:
GACGTTCAGTCCACAGTGTCC
R:
CTGGGAGTCTTCGGATGGAGG
Band lengths:
356-1257
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)