RnoINT0107083 @ rn6
Intron Retention
Gene
ENSRNOG00000009448 | Papln
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:RGD Symbol;Acc:1311176]
Coordinates
chr6:107260343-107261423:+
Coord C1 exon
chr6:107260343-107260550
Coord A exon
chr6:107260551-107261240
Coord C2 exon
chr6:107261241-107261423
Length
690 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
GCTGATAGCTGTCCTTACAGTGC
3' ss Score
2.79
Exon sequences
Seq C1 exon
CTGGAAAGTAGGACCATGGACGCCCTGCTCAGTCTCCTGTGGGGGTGGATTCCAGTCTCGCTCTGTCTACTGCGTGTCCTCAGATGGCACTGGTGGCCAGGAAGCTGCTGAGGAGACCCAGTGTGCTGGCCTAGCTGGGAAACCCCCTACCACACAGGCATGCAACCTGCAGCGCTGTGCAGTCTGGAGCGTGGAGCCCTGGGGAGAG
Seq A exon
GTGAGACCCTGCCTAGGACTAGGAGCTGTGTCCTGAACCTGGGTTTGAAATGCTTGCCTTCTGCTGAGGTCCTCAGAGGGTAAGGGACCTAGCTGGCCATCTTGGAAGACATGGCCAAAGCTGGGGTGAGACACAGCTTCCAGATTCTGGTCCAGGGTTCTCCTACAATCTCTAGCATCCCAGGGTTAGATGGGAAAGGGTTTGCCTTGGCTGGAAGCCAAAGCTAGGCATGCTTGAGGGTAAGGGTCTCCTGTGTCCACTGAACGCAAGTTGCATTACAGGGCTTGAAGGCTGGCAAGACAGCTCAGTGGTTAAGAACGCTTGCTGCTCTTCCAGAAGGACCTGAATTTGACTCCTGACCCTCATGTCAGGTTTTTCCACCTATAACTCCAGTTCTAGGGGATCAGACACCCTCTTCTGGTCTCACTGACATGCACATGAGTAGCATACACATGGAGAGACATGCATATACACATAAATCGAAACAAATCTAAAAATAAAAGGAGTGAGAAAAGCATTCTTCAGGCTGTGCAACCTCAGAACAGTGACTCAGCCTCTCTGGGCTCAGGAGTGGGATAAGGGCACGAGAGTGCCATCTGCCCCCTGAGCCAGGCTGGTAGGCCTCCAGCTGTCCCAGCTGACCTGGCTCTCCAGGGCTGGGGACCTCCCTGCTGATAGCTGTCCTTACAG
Seq C2 exon
TGCTCAGTTACATGTGGAGCTGGCATCAGGAAGCGGAGTGTCACATGCCGAGGGGACGAAGACTCTCTGGTCCACCCCGCAGCATGCTCCTTGAAGGACCAGCCAACCCTCACAGAGCCCTGTGTGCGAGAGGCCTGTCCTGGGTTCCGTGGCCAGGCCTGGCATGTCGGCTCGTGGAGTCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009448:ENSRNOT00000012757:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.076 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009014=TSP_1=WD(100=82.9),PF0009014=TSP_1=PU(13.0=10.0)
A:
NA
C2:
PF0009014=TSP_1=PD(83.3=73.8),PF0009014=TSP_1=PU(12.0=9.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGATTCCAGTCTCGCTCTGT
R:
TAGACTCCACGAGCCGACATG
Band lengths:
346-1036
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]