DmeINT0022241 @ dm6
Intron Retention
Gene
FBgn0053087 | LRP1
Description
The gene LDL receptor protein 1 is referred to in FlyBase by the symbol DmelLRP1 (CG33087, FBgn0053087). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 2R:8174165..8226438. Its molecular function is described by: calcium ion binding. The biological processes in which it is involved are not known. 20 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: viable; fertile. 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 late larval stages, during early pupal stages.
Coordinates
chr2R:8209714-8210336:+
Coord C1 exon
chr2R:8209714-8209836
Coord A exon
chr2R:8209837-8210084
Coord C2 exon
chr2R:8210085-8210336
Length
248 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
TAATATCCACTTCTGAATAGATA
3' ss Score
3.81
Exon sequences
Seq C1 exon
GTCCGAATGGCGATACGCCCAAGTGCCGCGCCTTCGAGGGCCAGTGCCGCAACGGCGACTGCCTGGAGTTGTCCCGCTTCTGCGACGGCCGTTGGGACTGTGATAACGATGAGCTGCAATGTG
Seq A exon
GTAAGTGCAGCCGATCGATTCGGCTAATTGGGCTGCCATAGCCAACACAATCGTCGTACAACATGCTGTTCCTAAACTAAAAGCAACCAAAATGGTTTGATATTTAGTTATACTGCTTGATTACAAAGTCGTAACTACCTTAATCAAATTGTTTTATTCTATTCTTATTCGGTACACACCATTTTGTTTCTTGAAAAAAAAAAACCCTTTCAAATAATCTCATAACGATAATATCCACTTCTGAATAG
Seq C2 exon
ATAAACAGAACGCTGCTTGTGCAGCACTGAACTGCAGCTTCAACTGCAAACTGACGCCGCAGGGGGCACGCTGCTACTGCCCCAAGGATCAGGTGCCAGAGTCGTCGAACTCCACCCGCTGCGTGGACTACGACGAGTGCTCCGAACCGGGCACCTGTGACCAGGTGTGCCGCAATACGCCCGGCTCCTACGAGTGCTCCTGTGTCTCCGGCTATGCGAAGACCAAGGGAAATCGCTGCCGGGCCATCAATG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0053087:FBtr0344893:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005713=Ldl_recept_a=PD(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=44.7)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0311204
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0311205
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:
CTGGAGTTGTCCCGCTTCTG
R:
CGATTTCCCTTGGTCTTCGCA
Band lengths:
296-544
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)