DreINT0110062 @ danRer10
Intron Retention
Gene
ENSDARG00000027867 | paplna
Description
papilin a, proteoglycan-like sulfated glycoprotein [Source:ZFIN;Acc:ZDB-GENE-070815-4]
Coordinates
chr17:51090111-51091569:-
Coord C1 exon
chr17:51091439-51091569
Coord A exon
chr17:51090235-51091438
Coord C2 exon
chr17:51090111-51090234
Length
1204 bp
Sequences
Splice sites
5' ss Seq
AAGGTTAGC
5' ss Score
5.61
3' ss Seq
ATCTGTCGGTGTGTTCTCAGCGT
3' ss Score
7.51
Exon sequences
Seq C1 exon
GAGAGAATCCCTGCGAGCTCAACTGCATCCCCAGAGGAGAGAACTTCTACTATCGGCAGAAGTCATCGGTGGTGGACGGGACGCCCTGCCGGCCCGGAGGAAAGGACATCTGTGTGGACGGACTCTGTAAG
Seq A exon
GTTAGCACGGCAATCTTTCATAAGTAATTGGAGTATATACATGGGGACTTTTATTTTGAATTTAACTGCTGTGCCATTATAAACTCACCACATTTAAGACCTGGTTTCTTTAAAATCTTCAGAATTATTCGCCCTCCTGTGATTTTTTTACTCCCAAATGAAGTTTAACAGATTCAGGAATTTCTCACAGTATTTACTATAATATTTTTTCTTCTGGAGAAAGTTTTATTTGTTTTATTTCAGCCAGAATAAAAACAGTTTTAATTGTTTTAAAGCCATTTTAAGGTCACTATTATTAGCCCCCTTCAGCAATATTAGTTTTGGACAGTCTACAGAATAAACCACTGTTATACAATGACTAATTACCCTAACTTTACCCTAATAGGGTATATGCCGAGCAAGTGCTGTTCCCATGCTGATACACTTCCGGTGTATTGTGAACTTTTTTCCATTTTATACGGTTCCTTATACAACATCGATGTTATAATGTCATTAAAATACATTCAGTTAAATAAACTTTAGTATTTATTTAGTTGCTCAAGCGTAAAATGAGACAAAAAGCTGTTTACTCGCACGCGCCCGTCAGAATCGGCAGGCTAACGTTGAAGCTCCATTGAATTTACTGGGGTAAAATAAATGCTCATATTATAAAGATACGGCGGGGGAAATGTAATTTAATGCAGCGCTTCTTGTACAATCTGAGACCCACTTTAAATCGGATATCACTCAGCCAGTGGAGATTGCTGATTTTTAAAGAAAACAGACCTTAAACGCACCGGATTCTGCATTAGCATTCAATTCGCAGGAAGCGCTTAACCCAGGTTACTGGCAAATTAAAAGTCCTATTAGCATGCTTCGGCATATACCCCATTACCTTAGTTAATGAACTGAACTGAACTGAGCTGAACTGAACACTAAAAACTGAACTACACTGTTCCAATTTACTATGACCATTTATGTAAAGCTGCATTGACACAATCTACATTGTAAAAGCGGTATACAAATAAAGCTGAATTAAATTGAATAAACCTGATTCCGCACTTTTGGATGGAAACACTGAACAATGACATACAAACATAAAGCCTTTAGTTTCCTGTTTGAGATTTCTTCAAATCCATAAACAATGTTAGAATAGAGCAGCGGAGCCTTGCTGCAAGCTGCATTTCTGCTTGAGTCTTTGTTTTATCTGTCGGTGTGTTCTCAG
Seq C2 exon
CGTCTGGGTTGTGATCATATGCTGGAGTCGCCGCAGGAGGAGGACGCATGTCTGCAGTGTGGAGGAGACGGACAGTCTTGCAGTCGGCTCAAAAACAGCTTCTCCATGCGCAACCTGCCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000027867:ENSDART00000154532:7
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:
NO
A:
NA
C2:
PF059869=ADAM_spacer1=PU(12.1=33.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAGAATCCCTGCGAGCTCAA
R:
AGGTTGCGCATGGAGAAGC
Band lengths:
246-1450
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]