DmeINT0018259 @ dm6
Intron Retention
Gene
FBgn0032979 | Clamp
Description
The gene Chromatin-linked adaptor for MSL proteins is referred to in FlyBase by the symbol DmelClamp (CG1832, FBgn0032979). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 2L:22165720..22169143. Its molecular function is described by: nucleic acid binding. The biological processes in which it is involved are not known. 17 alleles are reported. The phenotypes of these alleles manifest in: wing; polytene chromosome. The phenotypic classes of alleles include: viable; lethal; visible; some die during larval stage; developmental rate defective; lethal - all die before end of P-stage. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed at stages throughout embryogenesis.
Coordinates
chr2L:22165966-22167238:-
Coord C1 exon
chr2L:22167050-22167238
Coord A exon
chr2L:22166988-22167049
Coord C2 exon
chr2L:22165966-22166987
Length
62 bp
Sequences
Splice sites
5' ss Seq
TAAGTAATA
5' ss Score
-1.05
3' ss Seq
TTACCGTTATCTTTACATAGATG
3' ss Score
7.48
Exon sequences
Seq C1 exon
AAATCCGTCCAAACCCTTCAGTTGTAATATATGTGGTGGTCTGTTTTCACGTTACTCAAGTCTGTGGTCCCATAAAAAGCTGCACAGCGGTGAAAAAAACTACAAGTGCAGCATCTGTGGATTGGCCTTTGCTAAAGCCGTATATTTGAAAAACCACGCGCGCATTCATACAGGCGAGAAACCCTATAA
Seq A exon
GTAATACCAATCTTCTACTTGAAATTATACTCTTTATACTAATTACCGTTATCTTTACATAG
Seq C2 exon
ATGCCAAACCTGCGGCATGCAGTTTTCACAGTCACCACACCTCAAGAACCATGAACGCACGCACAGTGGCGAGCGGCCCTATGTGTGCGGTGTTTGCGACAAAGGATTTGCGCGCCACGCTACTCTTTGGAATCATAGGCGCATTCACACGGGCGAAAAGCCATACAAGTGTGAAATTTGTGGATCGGCCTTTTCTCAGGCGGCGCACCTTAAGAACCACGCAAAGGTGCACTCCGGAGAAAAACCCTACAAGTGCGAGATTTGCTCTGCAGCATTCGCTGATCGTTTTGCACTCAAGCGTCACCGCGGCATACACCAAAAGTACGGCCAAACTGCTCCTCGCCAGACCAGCAGCGATGGGATGATAGTGCATAAGCAGGAGATTCCTGACATGGAGGATGAGGCCCAACAGGAAGTGATTATCGGTGGGTTATAGATAGTTTAAATGCAGAGGTGACAGGCAGCTTAATGAAGTCACAGACACTGGAGTCCACCCTGCTTAGCTTCAGTTTATCGAGCGTTACTATGATCATCTGCCTCCACCTATGCTAGCCCCAGAACCATCTCTAAGGGCGCATATATCACCACAATGATATTAAAGAATAGAAAACGATGTTCCATCGTTAACACTTCAGCTGCATATGTCCTTTCTCCACTTTCATGTGGGATCTTCAAAAATGGGCGAAACCCAAAAACGCTTTTTACGATAAGCATACAAATGAACCTAATTTATTTGATAGCTTGTATAATATACTTAAACATCTTTAAACATTAAACGCATATATGTATAGGCATCGTATTTATAAGTGTTATAGGCTATTCTCTTATACAAATTGTAGGTGTAAAATATGGATTTATTAGGTGACGATACGAGCAAATCCGATACGTATGAATATGCACAGGTAATAAACACACACATATAAGTTGAAAGTTGTAAGCTTAAATATATTTTAATTAAATCTATCTAATATAAGTATGTATTAAATAATGCATAAAATCAAATAAATATTTGAATAAAATAC
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0032979:FBtr0085964:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.279
Domain overlap (PFAM):
C1:
PF134651=zf-H2C2_2=WD(100=40.6),PF134651=zf-H2C2_2=PU(57.7=23.4)
A:
NA
C2:
PF134651=zf-H2C2_2=PD(38.5=6.8),PF134651=zf-H2C2_2=WD(100=17.8),PF134651=zf-H2C2_2=WD(100=17.8),PF0172213=BolA=WD(100=31.5),PF134651=zf-H2C2_2=WD(100=17.8)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0099821
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0085317
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:
CAGCATCTGTGGATTGGCCTT
R:
TGCGTTCATGGTTCTTGAGGT
Band lengths:
140-202
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)