DmeINT0030852 @ dm6
Intron Retention
Gene
FBgn0015924 | crq
Description
The gene croquemort is referred to in FlyBase by the symbol Dmelcrq (CG4280, FBgn0015924). It is a protein_coding_gene from Dmel. It has 6 annotated transcripts and 6 polypeptides (1 unique). Gene sequence location is 2L:448254..453024. Its molecular function is described by: scavenger receptor activity. It is involved in the biological process described with 9 unique terms, many of which group under: cell death; programmed cell death; cellular component organization or biogenesis; membrane invagination; myeloid leukocyte activation. 18 alleles are reported. The phenotypes of these alleles manifest in: hemocyte; larval dorsal multidendritic neuron ddaC. The phenotypic classes of alleles include: phenotype; increased mortality; increased mortality during development; immune response 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 00-06 hour embryonic stages, during late larval stages, during early pupal stages, in adult female stages.
Coordinates
chr2L:449435-450878:-
Coord C1 exon
chr2L:450666-450878
Coord A exon
chr2L:450541-450665
Coord C2 exon
chr2L:449435-450540
Length
125 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
TGAACTTAATCTTTACCCAGGGC
3' ss Score
5.71
Exon sequences
Seq C1 exon
ATGCAACTAACTGCCTAGGGCTGGATTATTCCCACCTTGGCTATTCCTTAAAAGCGTGAACCTTTGGAATCCTACGTATCCACCATGTGCTGCAAGTGCTGCGGGGAAACTCAACGAAAGGTCTGGGTCTTCGGCTTGGGATCGGTTTTCCTTTTGCTGGGAATACTAATCGTGGTCTTCTGGCCGGGTATTGCAGATAACCTTGTAGAGGAT
Seq A exon
GTAAGTATATTTAGCCGTCCGAGATTGCGTATTACAGGTTCAGGGAAATATGTTTACCGAACGATAACTAAAAAAAAAAAAGATTTTCATTTCGACATACTAAAATGAACTTAATCTTTACCCAG
Seq C2 exon
GGCCTTACCCTCAAGCCCGGGACTGATGCCTATGAAAGCTGGCTGGAGGCACCTATCCCCATTTACCTGAGCTTTTACATGTTCAATTGGACGAATCCCGAGGACATAAGGAACCCGGACATTAAGCCAAACTTCGTGGAAATGGGTCCGTACACCTTCCTGGAAAAGCACAAGAAGGAGAACTATACGTTTTACGATAATGCAACGGTGGCATATTATGAGCGCCGCACATGGTTCTTTGATCCGGAGAGATCCAATGGCACATTGGACGACATGGTGACTGCTGCCCATGCCATTACCGCCACGGTAGCGGATGAGATGCGAGACCAGCGCAAGATCGTCAAAAAAATCATAAACTTTATGCTGAACCATGAAGGCGGAAAGTTGTACGTAACCAAGCCGGTGGGCGAATGGATCTTCGAGGGTTACCAGGATAACATTACCGATTTCCTAAACCTGTTCAACACCACAAAGATCGACATACCCTACAAACGCTTCGGGTGGCTGGCGGACCGCAATGAGTCGCTGACTTACGATGGCTTGTTTACTATTCACACGGGCACTGACGATATATCTAATCTGGGTAGACTTACCCACTGGAATGGAAAATCAGAAACTGGATTTTACGAGATGCCTTGTGGCATTGTTAATGGAACCACGGGCGACATGTTCCCGCCAAAGATGAATGTAAACGATGAGATTACGATTTTTGCCACCGATGCTTGCAGATTTATGAACCTCCGGCCCCGGGGCACATACGAGAATCACGGCCTGACCGCCACTAAGTGGGTAGGCACCGAGGAGACTCTGGACTCCGGAGAAAACTACCCTAACCAGGCGTGCTTCTGTGATGAGGCGCGATTTGATGAATGTCCCAAGACCGGTGTCGTGGAGTGCAAGGCGTGCCGAGACAAAGCACCCATTTACTCCTCCTTCCCTCACTTTTACCTAGCGGATCAGTCGTATGTTGATGCTGTCAGTGGAATGAAGCCGGAGAAGGAGAAGCACGAGTTCTTCCTAGCCGTGGAACCGATTACTGGAGTGCCTGTCCAAGTGCATGGACGCATCCAGATTAATATGATGATTGAGCCCGATGACGACTTCGA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0015924:FBtr0078087:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.016
Domain overlap (PFAM):
C1:
PF0113016=CD36=PU(6.1=65.1)
A:
NA
C2:
PF0113016=CD36=FE(79.8=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0077747
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0077748, FBpp0293283, FBpp0303674, FBpp0303675
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:
TCTGGCCGGGTATTGCAGATA
R:
ATGCCACCGTTGCATTATCGT
Band lengths:
249-374
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)