DmeINT0018188 @ dm6
Intron Retention
Gene
FBgn0035533 | Cip4
Description
The gene Cdc42-interacting protein 4 is referred to in FlyBase by the symbol DmelCip4 (CG15015, FBgn0035533). It is a protein_coding_gene from Dmel. It has 12 annotated transcripts and 12 polypeptides (10 unique). Gene sequence location is 3L:4322491..4364102. Its molecular function is described by: GTPase activating protein binding; lipid binding; phospholipid binding; protein binding. It is involved in the biological process described with 13 unique terms, many of which group under: macromolecule localization; plasma membrane organization; membrane organization; mesoderm development; germ cell development. 36 alleles are reported. The phenotypes of these alleles manifest in: multicellular structure; organism; cell junction; cellular anatomical entity; integumentary system. The phenotypic classes of alleles include: increased mortality during development; phenotype; increased mortality; neuroanatomy defective. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed within 00-18 hour embryonic stages, during early pupal stages.
Coordinates
chr3L:4325061-4327170:-
Coord C1 exon
chr3L:4326984-4327170
Coord A exon
chr3L:4325411-4326983
Coord C2 exon
chr3L:4325061-4325410
Length
1573 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CCAAGCTGTAATTGGCACAGAAT
3' ss Score
1.1
Exon sequences
Seq C1 exon
ATATCAATCTGGTTTCACGCCACCAAGGGACATACCCTTCGAGGATCTGTCCAAGTGCGATCCGGATTCCGTGCAGGACTCACACTACAGCAACTCGACATCGAACCACCTGACCATTAGAGGCACGATGAGTGCCAACAAGCTGAAGAAACGCGTGGGCATTTTTAACATATTCGGCAGCAATAAG
Seq A exon
GTGAGGCAGTCCGTGGCCAATTCGAGGGGCCTAACTTTGGGATACCTCCTCAGTGGGTTTTAGACTCGACTACCACTGCCTGACTATCTCTATTGTCCAGAGTTTTCAGTTCGCCGCACTTGTCCGTTCCATTCTGTGCACTAGCCTCTTGAGTTGAGACGCTTCTTGATTAGTTCTTAAGTTCGATGTTCTATTGATAAGGTGTAGGTCTTGGTTATGGTTTGTGTCTCTTTATGGTTTACTCATCCAGTCTTCTCTCTTTTCCGTTCTATTTCTATATTAATTTGATCGAATCTCGATTACCATATCTTTATTTCACTTGGACATGGTTCTGTCTCTTGCCGTAAGTACCAAGTGTCCAAAGAATTCGATTCGTGTCCTATCCAATCATAGTCCACAACCAGATCGGCATTTCCATATATACATACATCGCCTCATTCCTCGGATTGCTTTTGAATTGCCATGTTTTGTGTCTTTCGCTATTACTAATACTTTGTGCTTTAAGTTCGCTCCTCACCGACTGCAACATTATTCCAAATCCAAAGCTTCTTCTATAACTCACGAATATTAATTGATTAACTCTTGATTTCTACTTTTGTACACATATTTGTTGCTGCCATTCGATTTTAAAATGATTAAATGCTTAAAATCACACGAACACAACAACACCACACATGTGATACAATTGCAAAAATTAAAAACCTACAAAATAAATATTAAATCAATTCGCTGCCAATAGCAACGGCAGATAATTGAAGCCTGTATCACCATGAAGGTATGATGAATCTTTCAGCTTTCTCCCAACTAAATAACTAACTTTAACTAAGTCTAGCCTAAACTAGCCCCTTACGATTAATCTTAATAACACCACTATCTCGCTATTTACTAATCACAATCAGCTAAATAAGAATCTAATCATCACTAGCAATATCGTTTCCATTAACAATAATTAATAGTCTGAGCAACTTTCACTTTAAACGCCTGAACGCAAATGATCGGCATATTCTTGGCTTGATTAAACATAGTCAAGTTCTAAAAATGAACACCACCAATTATTCTCAAATAGTTAAGCCTTTAAATTAACCAGTAAATTGTTGGCCAACTAGCTGAAAGTCACAGCAGCACACTTACACATTATTCCATTTATGTTTTAACTTTATTATTGTTTAATTTCTGTTCTTTATGTGCCATTAGCTCTCGAATCCCACCGCATGATTGAATGCCTTTATCGCCTTGTTTTCCCTTTCGTTCCATTTCCATAATTTTTCTTTATGGTGCCATTTAATAGCCTGTTGATTTCGAAACTGGTTTGATTTATGTCGAAAGCGGGTCATTGGATTATCAAAAAATCTGCATTTATTATTTTGCTGTGTTGATATTATTATCTGATTTTTCGGTTTCCTCTGTTGTTTGTACTGATTCTAATCACTGCGTGCAGCTCTTGTTGTGTCTTGTGAATGTCTTGTGTCTTTTTAGTCCTGATTTGTATCTTATTATTCATTGCATTGGCCTATAAAGATATCATTCAATATACTTGTAATGCATTCAACTAACCAAGCTGTAATTGGCACAG
Seq C2 exon
AATTCCCTGACTGCGGATGGACAAAAGGAGGACTTCAGCGATCTGCCACCGAATCAACGAAGAAAGAAACTGCAGGCGAAGATCGCCGAACTGACACAGAATATCGCCCAGGAAACAAAAGCACGGGATGGCCTGATGAAGATGAAGATCGTCTATGAGGCGAACTCATCGCTGGGCAATCCCATGACCGTCGAGGGACAACTGAACGAGTCGGAACACAAGTTGGAGAAGCTGAAAGTGGATCTAAAGAAGTACCAGGGCTTCTTGGAGAAGGCAAGCCAAGTGCCGACGGCCACCAGTAGTCCGCAGGCGAGTCGAAATCAATTGCAAAACGGTCACCGAACCTCTAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0035533:FBtr0073339:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.450 A=NA C2=0.865
Domain overlap (PFAM):
C1:
PF154561=Uds1=PU(0.1=0.0)
A:
NA
C2:
PF154561=Uds1=PD(97.7=78.7),PF0157614=Myosin_tail_1=PU(91.4=98.1),PF0218511=HR1=WD(100=64.8)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0112051
Other Inclusion Isoforms:
FBpp0297233, FBpp0300521, FBpp0300522
Other Skipping Isoforms:
FBpp0073195, FBpp0297231, FBpp0297232, FBpp0297491, FBpp0297492, FBpp0305747, FBpp0305748
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:
GATCTGTCCAAGTGCGATCCG
R:
ACTCGTTCAGTTGTCCCTCGA
Band lengths:
355-1928
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)