DmeINT0037631 @ dm6
Intron Retention
Gene
FBgn0003742 | tra2
Description
The gene transformer 2 is referred to in FlyBase by the symbol Dmel ra2 (CG10128, FBgn0003742). It is a protein_coding_gene from Dmel. It has 8 annotated transcripts and 8 polypeptides (4 unique). Gene sequence location is 2R:14602004..14604337. Its molecular function is described by: identical protein binding; RNA binding; mRNA binding; pre-mRNA binding; protein binding. It is involved in the biological process described with 12 unique terms, many of which group under: developmental process; reproduction; developmental process involved in reproduction; cellular component organization or biogenesis; male somatic sex determination. 70 alleles are reported. The phenotypes of these alleles manifest in: abdominal sternite 6; female genital disc; segment of leg; female genitalia; adult prothoracic segment. The phenotypic classes of alleles include: phenotype; fertile; visible; sterile. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of moderate expression. Peak expression observed within 00-12 hour embryonic stages, during early pupal stages.
Coordinates
chr2R:14603348-14604123:-
Coord C1 exon
chr2R:14603984-14604123
Coord A exon
chr2R:14603502-14603983
Coord C2 exon
chr2R:14603348-14603501
Length
482 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAT
5' ss Score
8.76
3' ss Seq
CCATTCCACATCGAATCAAGGTC
3' ss Score
2.38
Exon sequences
Seq C1 exon
TTTCGATAGGTAAGCAAAAAGCCAATGGATCGGGAGCCACTCAGTAGCGGGCGTCTCCATTGCAGCGCCAGATATAAACACAAGCGATCGGCGTCATCATCGTCAGCGGGGACAACTTCATCCGGACACAAGGACCGCAG
Seq A exon
GTAAATGTGTACACACATATGTGAGACGACCCTAAACGATACCTCTTTTGACATGAAGCATCGAGTAGTTTTGACTGGCAGTTTGGAAAAAAGGTTCAACTGTCATAGGGCCCTTTCATTTGGATTTGCCCCCTCAGCCGATTCAGCTGGTGCTCTTGCCAAGAAAGTTAAAACCAAAAATCATTCAAGCCGATTTCATTTCATTGGAAGAAACCAACCAACCAACCAACCAACCAACGAACATCACTATGTAAGAACCCACCGAAGCAATCATTTTCATTCTACGTCCAACTACCAAAGAATTTGGCCGAAAGAGGTCGAACCCAACCGTAGCATTTGTCAAGTCACACAAATTTTCCAACTGTCAGTTACCAAGGCGTGCAAGAACCACCCGAAATCCACACGAAATACAAAACTTTTCAAGACCCTCAAGAACGAACCGCAAGATAATCTTATTTCATTCCATTCCACATCGAATCAAG
Seq C2 exon
GTCTGACTACGATTACTGTGGCAGTCGCCGGCACCAGCGGTCCTCCTCTCGCCGACGCTCCCGTTCGCGTTCCTCCTCGGAGTCGCCGCCACCGGAGCCGCGTCATCGCTCCGGACGTTCATCACGCGATCGCGAACGAATGCACAAGTCTCGC
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0003742:FBtr0089617:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.987
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
FBpp0088560
Main Skipping Isoform:
FBpp0088562
Other Inclusion Isoforms:
FBpp0088561, FBpp0088564
Other Skipping Isoforms:
FBpp0088563, FBpp0088946, FBpp0088947
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:
GCAAAAAGCCAATGGATCGGG
R:
GAGACTTGTGCATTCGTTCGC
Band lengths:
279-761
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)