DmeINT0011611 @ dm6
Intron Retention
Gene
FBgn0261999 | CG42817
Description
The gene Ca[2+] channel Muscle-specific alpha2/delta subunit is referred to in FlyBase by the symbol DmelCa-Ma2d (CG42817, FBgn0261999). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (1 unique). Gene sequence location is 2L:16231475..16241527. Its molecular function is described by: voltage-gated calcium channel activity. The biological processes in which it is involved are not known. 8 alleles are reported. The phenotypes of these alleles manifest in: sarcomere; M band; nucleus; embryonic/larval somatic muscle. The phenotypic classes of alleles include: flightless; viable; fertile; locomotor behavior defective.
Coordinates
chr2L:16235620-16237310:+
Coord C1 exon
chr2L:16235620-16236949
Coord A exon
chr2L:16236950-16237133
Coord C2 exon
chr2L:16237134-16237310
Length
184 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGA
5' ss Score
10.65
3' ss Seq
TATTATATTTTTCCATACAGTAC
3' ss Score
7.67
Exon sequences
Seq C1 exon
TGTCGGCAAGTGGGCCACCCAATTTGGCGACGAGCTGTTCGCGCTGGCGCAGAAGATCACCAAGTCGCAGGAGATCAAGGAGAAGTACAAGGAGTACAATGCCCGCGTGGAGCTGAAGAACGGCACCGAACTGATTAAGTCAATAACGAAAAATGTGGGCAGAATGCTGGCGAGGAAAATGGACGCGGTGCGGTGCATCCAGGAGCGTGCGGAATATGTGAACGAGAACTTTGAGTTTAATCTCACCTATGCGCTTCAGAACTTCACCTACTTTTCTAGCAAGTATTCGACCTTTAATGGAAACAGTTCCGAGGAGCTGGAACCTAATGAGGCTGAGTTCGCCTGGATGTATCGGAATATGGAGTTGAATCCGGACACACACTTCTACAATACGCCAGTGGACACGGAACACAGTTCGGTGCACGTGCCATCGAATATATGGGATCGATCGGAACGTGTCCTGAAGACCATAATGTGGTCCGAGCATCTGGACGAGGTGTTCCGGCAGAATTACCAATCCGATCCGGCCTTGTCGTGGCAGTACTTTGGCTCCGATACGGGAATCCTGCGCCACTATCCGGCTGCCCAATGGACTGATACCAGACCAAATCGGGATGATGCCGACACCTATGATTGCCGCAAGAGGTCTTGGTACATTGAGACAGCCACGTGTTCAAAGGACATTGTCATCCTGCTGGATCATTCGGGTTCAATGACGGGCTTCCGGCATCATGTGGCAAAGTTTACCATTCGCAGCATCCTAGACACTTTCTCCAACAATGATTTCTTCACCATTCTGCGGTACTCGAGTGAGGTAAATGACATAATACCCTGCTTCAATGGAGCTCTCGTCCAGGCGACACCCGAAAACATAGAGGTCTTCAACCAGCAAATCGAACAGTTGGACGATCCTGAAGGATATGCTAATCTCACCTTGGCCTACGAGACGGCCTTCCAACTGCTGCGAAAATACTACGATAGTCGTCATTGTGTCACCAATTCGACGTGCAATCAGGCCATTATGTTGGTCACCGACGGAGTGGCTGGAAATACCACCGAAGTCTTTCAGAAGTACAACTGGGGCAATGGCGAGAATGGAACCTCGCAGATGGACACACGTGTGTTCACCTATCTGCTGGGCAAGGAGGTCACCAAGGTGCGCGAAATCCAGTGGATGGCCTGCCTCAATCGGGGCTACTACTCGCATGTCCAAACTTTGGATGAGGTCCACGAAGAGGTGCTCAAGTACGTCGATGTCATTGCCACGCCCTTGGTGCTGCAGAACGAACAACATCCGCCCACCTGGACGCACGCCTTCACGGACAAAACG
Seq A exon
GTAAGAGTTTATAGTCATATTTTAAAATGGTTTCACAATATTAACTTTAAGTCCTTGGAGTAGTTATAATTTGGATCCATTTTTATATTTATAGGGCTGATATCAAACTTGTGTGTGTTTTTATTCCATTTCATAACCATTATTTAATTTATAAACATTAACAATATTATATTTTTCCATACAG
Seq C2 exon
TACGATCCAAAAACTTCCAATGAAAAACGACCTCGCCTAATGATATCCGTGGGAGTGCCCGCCTTTGATCGCTTCTATCGCCACGCGAACAGCACAAATCCGAGGGCACGTTTGTTGGGAGTCGCTGGAACAGACGTGCCCGTGGAAGATATAGACAAGCTGACACTGCCCTACAAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0261999:FBtr0303797:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.050 A=NA C2=0.153
Domain overlap (PFAM):
C1:
PF083996=VWA_N=WD(100=28.8),PF135191=VWA_2=WD(100=43.0),PF0274313=Cache_1=PU(8.0=1.8)
A:
NA
C2:
PF0274313=Cache_1=FE(58.0=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0292804
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0304633
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:
TACGTCGATGTCATTGCCACG
R:
GTAGGGCAGTGTCAGCTTGTC
Band lengths:
258-442
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)