DmeINT0025952 @ dm6
Intron Retention
Gene
FBgn0010258 | Rbp4
Description
The gene RNA-binding protein 4 is referred to in FlyBase by the symbol DmelRbp4 (CG9654, FBgn0010258). It is a protein_coding_gene from Dmel. It has 2 annotated transcripts and 2 polypeptides (1 unique). Gene sequence location is 3R:13654556..13656394. Its molecular function is described by: single-stranded RNA binding; RNA binding; mRNA binding; mRNA 3'-UTR binding. It is involved in the biological process described with: mRNA processing; germ cell development; regulation of RNA metabolic process. 7 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: female fertile; male semi-fertile; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of extremely low expression. Peak expression observed during late larval stages, at stages throughout the pupal period, in adult male stages.
Coordinates
chr3R:13654789-13655880:-
Coord C1 exon
chr3R:13655597-13655880
Coord A exon
chr3R:13655485-13655596
Coord C2 exon
chr3R:13654789-13655484
Length
112 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
CTGCTTGCTTTGATTTTCAGCAC
3' ss Score
7.8
Exon sequences
Seq C1 exon
AATTGTGGAGACCAAGCACGCACTGCCACGTCAAGATTTCAAAAGGGGTGGCGGCGTTGGTTCCGTTGTCGGAAGTTTTGGCTGTGAAGCCGGTTTCATGAACTCGAAAAGGATCTTTCTGGGCGGCTTGAAGGAATACCACGATGAGAATATCGTACGCGAATACTTTTCGCAGTTTGGCCCTGTGGCCAGCGTGAAATTGCTCATGGACAGGGAGACCGGACGTCAGCGGGCATTTGGCTTCCTCGAGTTCGTGGATCCATCCAGTGCCGAGAAGGCATTGG
Seq A exon
GTAAGTTTCCATGTTTCTCATTTATTGAAAGTCATCGTGCATTTTTTTCAACTACCTTTAAGTATGATATAGATTAAAATCTGATGATAACGCTGCTTGCTTTGATTTTCAG
Seq C2 exon
CACCGCGCAAGCACTGGATTCTTCAGACATTGGTGGAGGTGAAGAGATCCACCCAGAAGGCCGACAGGCGTTTTCGGTTCCCCATATTTAGCTCGGTTCGAGCCGGCTACATTCCGCCCCAGCCGGCCACTGCTGATAGCTACAATTACAACAATCCCAACTACAATCCCTATCTGGCCCAATCCGTCCTGCCGCCATCGGCATTCACTAACGGCTGGGCCCACTATGTAATTCCGATGGCACCCAAGCCAACACCCGGACAGAACATGGCTGCTTCGTTGCCGTCACAGCAGCTGGCAGAGCACTCGCTCAACGGACACGGTCCGGACATGTGGTCCTCCTATCCGAAGACCGGTATCTACTCGGCCCAGGAGTGGACTTCCAGCAAAGTGGCCGAATGGGGACCGAAGGCCGGGCACAAACATGCCCAGACATCGACCAACGATCGTGCCAAAATCGATTTGAAAGAACTCCAGGCAGCTACTTTCAATAACAAGCTGGATTTCGGCGCCCGTGGCGACGCGGATCGCATGTCGGGAGCTGGCTTGGGATTGGGTTTGACTGGCGGTGCCGCCGTGGGAGTTGGAGCTATTAAGAAGTGGCCCACCCAGGACTATAAGGTCTTCAAGCCAGCTAAATCTCCGACCAACGGAGTGATTCCGAAGATCGGCAAAGAGGCTACAACACCACCCTACG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0010258:FBtr0082853:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.031 A=NA C2=0.339
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(4.3=3.1),PF0007617=RRM_1=PU(87.7=59.4)
A:
NA
C2:
PF0007617=RRM_1=PD(10.8=3.0)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0082318
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:
TCGAGTTCGTGGATCCATCCA
R:
AGCCGTTAGTGAATGCCGATG
Band lengths:
255-367
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)