DmeINT0025362 @ dm6
Intron Retention
Gene
FBgn0003137 | Ppn
Description
The gene Papilin is referred to in FlyBase by the symbol DmelPpn (CG33103, FBgn0003137). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (4 unique). Gene sequence location is 3R:28520665..28540324. Its molecular function is described by: serine-type endopeptidase inhibitor activity; peptidase activity; extracellular matrix structural constituent. It is involved in the biological process described with: extracellular matrix organization. 9 alleles are reported. The phenotypes of these alleles manifest in: embryonic/larval tracheal system; embryonic/larval somatic muscle; Malpighian tubule. The phenotypic classes of alleles include: lethal - all die before end of embryonic stage; lethal - all die before end of pupal stage; some die during embryonic stage; some die during pupal stage; partially lethal; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of very low expression. Peak expression observed within 12-24 hour embryonic stages.
Coordinates
chr3R:28521542-28522632:-
Coord C1 exon
chr3R:28522482-28522632
Coord A exon
chr3R:28521701-28522481
Coord C2 exon
chr3R:28521542-28521700
Length
781 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGT
5' ss Score
9.73
3' ss Seq
CTTCTTTACGTGATTTATAGTTA
3' ss Score
5.27
Exon sequences
Seq C1 exon
ATCAACACGAACAAGGGACGATATGTGCTGACCGCCAACGGTGATCTGACCATTGTCCAGGTGCGCCAAACAGACGATGGCACCTACGTCTGCGTGGCCAGCAATGGTCTGGGAGAACCCGTGCGTCGTGAGGTCGCCCTCCAGGTTACAG
Seq A exon
GTGCGTTTCTAAGACCGCCTTCAATACATTTGTGTTTTTTGTTATTATTACTTAATGCTATGAATGTTAAGATCTCAATATATACATAAGTAGGAAATTAATGAATCGGATTACCGATTCTGCTATTCCTAATATCCACTGATACTTTATACACTTTGGTGATGGCTATGTAACTAACTGCTTTATATTGAACACTTTGCGCATGTTGCCTGCTTTCCGTAATTGCTTGCTTGAATCTTGGTGGCGGTAGAACCCGTAAGTCAGCCAGCTTACATCTACGGAGACAAGAACGTTACTCAGATCGTGGAGTTGAACCGTCCGGCAGTGATCCGCTGCCCGGCCGGTGGCTTCCCAGAGCCGCATGTCAGCTGGTGGCGCAACGGACAGATGTTTGGCCTGAAGAACAACCTGATGGCCCGCGACTACTCGCTGGTCTTCAACTCGATCCAGTTGTCGGATCTTGGCCTCTACACCTGCGAGGTGTACAATCAGAGGCGTCCGGTCTCGCTGCGCGTTACTCTGAAGGCGGTGGGTCCTGTCCGGCCTCTGAGTCCCGAGGAGGAGCAATACATGCAGTATGTGCTCAATCCGGCCACCCGTCCGGTGACCCAGCGACCCAGCTATCCCTATCGACCCACCCGACCGGCCTATGTGCCAGAGCCCACAGGTAAGTACTGCACCTTTGCATGTTTTCGCTGGGCTGGCATGGTGTTGGATTTTTTTTATTGTTTATGTATGTTCTGGTAACAAAAAACTAACCACTTCTTTACGTGATTTATAG
Seq C2 exon
TTAATGTTCATGCCGTGTTGGCTCTGGAGCCGAAGAACAGCTACACCCCAGGCTCCACCATTGTCATGAGCTGCTCCGTGCAGGGCTATCCAGAACCGAATGTCACATGGATCAAGGACGACGTGCCTCTGTACAACAACGAGCGTGTTCAAATTACAT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0003137:FBtr0300337:9
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:
PF0767911=I-set=PD(55.8=94.1)
A:
NA
C2:
PF0767911=I-set=PU(54.2=83.3)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0289566
Other Inclusion Isoforms:
FBpp0291051, FBpp0291052, FBpp0291053
Other Skipping Isoforms:
NA
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:
ATCAACACGAACAAGGGACGA
R:
ATGTAATTTGAACACGCTCGTTGT
Band lengths:
310-1091
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)