DmeINT0025697 @ 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:13989685-13990707:-
Coord C1 exon
chr2R:13990566-13990707
Coord A exon
chr2R:13989987-13990565
Coord C2 exon
chr2R:13989685-13989986
Length
579 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAAC
5' ss Score
4.68
3' ss Seq
CCATTTTTTTTTTATCAAAGTTT
3' ss Score
4.88
Exon sequences
Seq C1 exon
CTGGCAACTCTGGCCCTCACACACACTCAGTCGCCCCCCAAATGTATCGGAAACATGCAGCCGAGATAAAATAGTGAAAAACTAGTTACCAAACATAACCGATCAGTGCGGATAATAAGAATTGGCAATTCAAAATTAAATG
Seq A exon
GTAAACGAACGTCGGCGCGATTAATTAAACTCAACCATAGGAACGCGGAGAGAGTGGCCAGTGAAAGCCAGAACACTCTCTTTCGTCGGAGCGTCTGTGTGTGTGTGTGTTACGTGTGTGCGTATGTGTCTGTGTTGACAAAATACAACAAATCGCAGCGAAAACAGGAAGTGTACGAACGATAAAGCATAAGATTGCACATTTCGCATTAAAATAGGCGACAAAAACCCGGGGGCGCATGCAGATCCACACATTTCTGGCCCACTCACACTCACACAACGCAGATCAGGGGGCGTTTTTCTAGATCAGTGACCAAGTCTTATATGGCTTTATGTTTTGATGCTGCACTAAATATGGGTGAAACATCACGTCATTTATGCCACGCTCCTTCTCCAAAAACAAAGATCATGTTGATTTCACTGCATTTGAATATATATATATATATATACAATAGTTAATGTTCGTGTGCGTCATTCGCTCATCAGCTATATAGTATACGAGTGTTGTTATTGTGGATCGCTTTCGCATGTTAATGCTTTTGTGTGTTATTTTTTCCATTCCATTTTTTTTTTATCAAAG
Seq C2 exon
TTTCGCGCTATCGCCCAGTCAGCTCAGAAGCAGCCGCTCCCCAACTGAGAGCACAGAGAAACCAGCTCTGGCCACTTGCTCCTCCGGATCCGGCTCCTGCTCCTGTCCCCGATCCCCTCCCCCACCCGCCAAATCCTGATCCTGCTCCAAATGACTGACGGCGAACAGCAGGAGGCGCTGGTCAAGCGGGCCGAGGACGAGCGCGAGGACATCTTCCGGCGCTACGAACTCGGGCTGGATCCCAGCAATGTGGTGGACTCCTGGGAGAATCCCACCTTCGAGATCTACCACAGGACAGACAA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0020620:FBtr0087605:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.275 A=NA C2=0.275
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
FBpp0086730
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0086729, FBpp0086731, FBpp0303476, FBpp0303477
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:
CGGAAACATGCAGCCGAGATA
R:
CAGGAGTCCACCACATTGCTG
Band lengths:
358-937
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)