DreINT0110077 @ danRer10
Intron Retention
Gene
ENSDARG00000042186 | paplnb
Description
papilin b, proteoglycan-like sulfated glycoprotein [Source:ZFIN;Acc:ZDB-GENE-030131-6023]
Coordinates
chr20:33602163-33602905:-
Coord C1 exon
chr20:33602729-33602905
Coord A exon
chr20:33602314-33602728
Coord C2 exon
chr20:33602163-33602313
Length
415 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
TGTTGTCTGGTCTCCTTCAGTGC
3' ss Score
9.32
Exon sequences
Seq C1 exon
TGTTCAGTGACCTGTGGTGAAGGGCTGCAGACACGAGAGGTGATCTGTGTCGGGGCCAGAGGAGAGCGACTCTCTGAGCACCACTGCAGTGGACTCACGCGACCACAGGCCACCAAAGCCTGCAAGAGACCGGCCTGCCATCAGGTCTTCAGATACTACACCAACGACTTCAGCCTG
Seq A exon
GTGAGATGAAGGAGCAGAGGAAGAACCTTAAGGGGGATGTGCACTGTAAAAATTTCCACACAATCGATTTGTGTTGGGACAACATGAAGGAATTAAATTAACTTATTAGTGTTTTAAAATTTAAGTGGATTGAACATGAAACAATTACAGGTGAGGTTTATTTAACTAGGTTAATTAGGTTAAGCCATGGTCAATTGCTCTGTAGACAATCTGAAAAAATATTGGTTAAGGGGGCTAATAATATTGACCTTAAAAAATTGGAAACGGCTTTTATTCTAGCTAAAATAAATAAGACTTATACTTTGATATTGTGTTGTTTCAGCTCATTTTTAAAGAGCTTGGATCAACAAATGTCATTTTTTAAAGTGTAGATTGTTTTTGGATGTCATTGTTGTTGTTGTCTGGTCTCCTTCAG
Seq C2 exon
TGCACCCGGAGCTGTGGAACTGGCACCCGTGAGCGTAGAGTGGTGTGCATGGATTTGGATCAGCATCCTTATTCAGATGACAGATGTGCTTCTCTTTCCAGACCTCATGCTGTGGAGAACTGCAACACACAGCCCTGTCCTGGCCCGCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000042186:ENSDART00000061836:9
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:
PF0009014=TSP_1=PD(84.9=76.3),PF0009014=TSP_1=PU(11.3=10.2)
A:
NA
C2:
PF0009014=TSP_1=PD(84.9=88.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTCAGTGACCTGTGGTGAAGG
R:
CAGGACAGGGCTGTGTGTTG
Band lengths:
318-733
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]