DmeINT0014756 @ dm6
Intron Retention
Gene
FBgn0035842 | CG7504
Description
This gene is referred to in FlyBase by the symbol DmelCG7504 (FBgn0035842). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 3L:8131429..8137498. Its molecular function is described by: transcription termination site sequence-specific DNA binding; RNA binding. It is involved in the biological process described with: termination of RNA polymerase II transcription. 5 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: viable; female sterile; female fertile. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of very low expression. Peak expression observed within 00-06 hour embryonic stages.
Coordinates
chr3L:8133850-8135817:-
Coord C1 exon
chr3L:8134047-8135817
Coord A exon
chr3L:8133987-8134046
Coord C2 exon
chr3L:8133850-8133986
Length
60 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
CCTTAAATTCATTTTCGCAGGAT
3' ss Score
7.71
Exon sequences
Seq C1 exon
CCGACAGCACGACTCCGGATCTTCCAGCTGTTCGTAAATTATCCGTCTCATCTATTGATTCTGTATATGAAAATAAACAGACAAAATTAAACTCTAAGCTTAAGTCGTGCTTAAAGAGCCCGACCAAGACATCAGTAGATAACATGGAAAATATGACGGAAACCAAAAGTTGCTCAAACCGTCAGCGCGAGCAAATAGTTGCATCCCGAAATGAACCAACTAATATCTGTCCGCAAAAGATTGAGACTAACAAAACCTCAACCCGTAAGCGATTCGTATCGACCACTTCTCGGGATGAGTTATCTACCACTTCAAAAGAAATCAAAGATGCTCCTAAAAATAATGTGGAACCTCCTAAAAAAATGTTGCGCAGCCGTTCAAAATCCTGTTATATAGATAGGCCTGTGGAATTGGATGAACACATAACCAAAAATGAAGTGCCCCTTAAGAAGAAATATGAAAGTGTTGATAATAGTAAGGAAGAACTGATAGTAACCCTGGAGGCTCCAGCAATGTTAACGACACCTACTAAATCTAAAACCCAATGTGTTAAAAAAAAAGCAACGCAGACTCGCGGCAGACGAAAGACAATACACAGCCGTGATGAAATAAGATCCTTGACAGCTGAGGCTGAGGAAAATAAAAAGATTTCACCAGCAAAACAGACCAACGAAGAAATCCCTATTCCAACTAAAAGTCCTCTTAAAAGGAATGCGCGGCTGCTCAACCGATCAAAATCGTGCTATATGGATCGTCTGGTGATCTCGGAAACCGAAGATCCTGCCAAGAAGGTGATTAAGGATATATCTCCAACTAAAAGCGACACTACAGACAACGTTCTAAACTTTGTTGATGTGAGACAGACACGCGGCCCCTCTGTGATTGAGGCTCCATCCTTGCCCAAAAATCGAGGTAAGCTTCGAGGGGTCTCGGCTGAGGTGAAAGTTAAAGATAAGGTGCTAGATCGCCAGCGTTTTATTGACTATCAAGCCGAAATGAACGCTAAATGGAAGCAGAAACCCAAAGACAAGAAAAAAGAAGACGAAAAGCTAAAAGAGTGCCGCCGCGAAGCCCTCAAGAAGCTGTCTGAAAAACCAAAGGAAAATAGTCATCGTTCAACAACCAATAAGAGAAAGAATCCTACAAGTGTTCCCACCGTTCAAAACACCAATCGTGGCGGATTTTTAACGAAAGGAGTGGATGGCCCAGCCCCAAAACTGGCAAAGACGGATAACGCTAAGCCACCACCAAAGAAACCAGTTCCCAAACAACCACCCGCTATCGAAACGTTCTCACAGCAGCTCCAAGCAGCTGATAAAGCTGTTCTGCATCCGCAGCCACAGTGCTCGCGTCCAGTAGAACGGAAAGAAGCGGAGCTGGCGAGGAATCAGCGCACTTGTAACAAAGTTACCTTTGCTGAAATGGAGCTTTACCATCAAAAAGCCGAAGACTCAAAGAAGCTACAAAAGAAACTGCGTAAGGTGCATTTCAACGATGATGTGAAAGTACACTGTATCGAAAGGGTTAAGGGAGCCAGTTCTAAGGTTCAGGGCCGCAAGGAGTGCATAAAGCTCCGCCTCAGCTCCTACCGCGAACGCCGCGAATGGATTCGAAGGGAAAATAAACCAGTGAACGACATACGCCAGCACTCTCGGAGTATCCTAAAGTGGGCTAACCAATGGCTAAAGCATGGCAGCGTAGATGCGGTTGCTGAACAAGATGTCTTAATGCCCATTCCACCTGAATTTGATAGCTTTAAGAACTATAGAGA
Seq A exon
GTGAGTTGTTGATAGTCTTCTAGTTTCTACACTATTTCAACCTTAAATTCATTTTCGCAG
Seq C2 exon
GATATTTGTGCCCTTGATGAAACTGGAGCTGCTTTCCACCATCGAAAGAGACTACAAAATTAACAATAAAAACACTTTTTCGGTCAGCTTAATAAACGTTGAAACGCAGGATATGTGCTACCGTTTGGTTACCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0035842:FBtr0273367:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.720 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0271875
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0271876
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:
GCTAAAGCATGGCAGCGTAGA
R:
TTCGATGGTGGAAAGCAGCTC
Band lengths:
136-196
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)