DreINT0110047 @ danRer10
Intron Retention
Gene
ENSDARG00000027867 | paplna
Description
papilin a, proteoglycan-like sulfated glycoprotein [Source:ZFIN;Acc:ZDB-GENE-070815-4]
Coordinates
chr17:51080927-51081991:-
Coord C1 exon
chr17:51081865-51081991
Coord A exon
chr17:51080999-51081864
Coord C2 exon
chr17:51080927-51080998
Length
866 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGT
5' ss Score
10.65
3' ss Seq
TGCTGTTCCTGTTCTGTAAGGAT
3' ss Score
4.82
Exon sequences
Seq C1 exon
GATACCAGTCCCGTCTGGTCTTCTGCACGTTTGAAGATGAGGCGTACTCTGATTATCTGTGTGCGTCGCTCCCTCGACCTCTCAGTAACCGCACATGCAACGAGCAGCAGTGTCCACAAACCCGCAG
Seq A exon
GTACGTCAACACATTCATCCCCAAACTGACTTTGTGCTAACAACTGTGATTTCTTTAACCGTGTTTGTTTGATCAAAAGCTGATTTCATTACCCACACATACATTTAAAGTAACACTCCACTTTTTTTTTTTTCTGGAAACAGGCTTATTTTACCGCTCCCCTAGAGTTGTACAGTTGAGTTTTACCTTTTTTTTTGTGTCTGGCAGGAAAATATGTAGCTTAGCTTAGCATAAATCATTGAAGCGGAATAGACCGTTAGCATCGTGTTAAAAAAATTATCAAATTATGAGTATAAATAAGTTTGCTATTTTATAGTTATAGTAATAAGACTCATAGGAAGATTTAAAAATGGCTATTTTGCAGGCTGATACGAACTTTATACTCATTCTGGCGTAATAATCAAGGAACTTTGCTGTCGTACCATTGATATTAGTTAGTGCTTTTACCTAGTTATCTAGCTAGGGACTATTTTTAGGCTCTGTGTAATATCTTATATATATGGTACGGCAGTAAAGTTCCTTGATTATTATGCCAGAATGACAGTAAAGTTCCTATTGAGCTGCAAAGTGGCAACTTTTCATTGTTGTTGTTTTCACTTTCTCAATGTAATTACAGCAGAGTCATCCTTTATCAAAATCCTTTTTTGATTTTCTTTTGAGCGAGATGCTAATGGTCATATTTGATTTAATGATAAGCTAAAAGGGCCGGAGATCAGCTGAAAGGACTTTAAAATGACCGACCTCAACTGTTTAACTCTAGGAGAGATGTACAAATTGGCCAATTTCCAAAAGACCTTGAGTGTTCCATTGTTTGTGGAGAATCTTTGGGTCTCACACCTTTGGCTGTGCTGTTCCTGTTCTGTAAG
Seq C2 exon
GATGGCGTATGTGTACGAGGCGCAGTTGTGGAGGCCCACGGAAACACCACGAGTCTATGTACAAGTGTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000027867:ENSDART00000154532:12
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:
PF0009014=TSP_1=PD(71.2=86.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGTCCCGTCTGGTCTTCTG
R:
CACTTGTACATAGACTCGTGGTGT
Band lengths:
190-1056
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]