RnoINT0107095 @ rn6
Intron Retention
Gene
ENSRNOG00000009448 | Papln
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:RGD Symbol;Acc:1311176]
Coordinates
chr6:107268972-107270787:+
Coord C1 exon
chr6:107268972-107269109
Coord A exon
chr6:107269110-107270659
Coord C2 exon
chr6:107270660-107270787
Length
1550 bp
Sequences
Splice sites
5' ss Seq
CAGGTTCAT
5' ss Score
3.89
3' ss Seq
TGACTCTGTTTGGTCCCCAGGCA
3' ss Score
10.21
Exon sequences
Seq C1 exon
GCTACGTCTGGACCGGACTCAGCCTGGAGTGATAGATGCCAGTCCTGGCCAGCAGATCCAGCTCACCTGCCATGCTGAAGGCTTCCCAGTCCCCACCATTGAGTGGCAAAGAGATGGGCAGCTGGTCTCTTCTCCCAG
Seq A exon
GTTCATTCAAGCCCCCCACCCCCATTCTATGGAGACCAGAGCAGGCCTAGGTCCTGGAGAGACAGGGTTGGAAGAGAGGATGTCTGGGCATTTCCAAAGGATGGTTGACAGGCCAGCCAAGGAATGAGGCAGCTGTGCACGCCCTGGGCGGTCCCCACTGCTGGCTGATGTTTGCTGTCTGTTGTGGAAGCTGCAGGGTTATACAGGTCACACACAGGTGCTAAGTAGCACAGTTCACTACAGAATAGGGATTTGAGGCCGTTGGCACAAGGCAAAACAATAAATCTAAGCCTTCAATCCCAGCACCCTGGAGACAGAGGTAGTCTCTGTGAGCTAAGGCTAGCCTGGTCTACTATGGATTTCCAGGATAGCCAGGGCTACATAGTAAGAGCCATCAAAAGGAAACATATCCACTCCGAAACTCTAAAACCAAGTTCTCAGCACAAAGGAGATTGATTTATTTGTGTCTGAGGGACTAGGGGCAGAGAATAAGAGACAAAGACAGGAGCTAGAGGAGGAGGGAAATGGAGAAGGGGCAGAGATGTTTGTCCGACAGTGGGACAAAGGACTGTCTCTGGATAGAGAAGATATTGTCTCTGGTTAGAGTGGCCCATGTGGTTTATAAGGTACGAGAGGAAACCCTGTTAGGATGAGGTATTCAATTGGGCGTGTTAATTACATAAGCCAAGGGGGGCTTTTGATTGCTGGACATCAATACTTTGATAGCTGGACCTTGGTGGTCAGCCTTAGGAGGAGGAAGTGGCCGAGTAAGGGAACAGACCTTGGTGGCTTGTCCTGATAAGAATGGCTTTTGTTTTAATTTGGATTCTAGGGGTTGAACTTAGTCCTTATGCCTGCATGACAAGCACTGTGTTATCTCCCTAGACATCTTTGTGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTTCTAAGACAGGGTTTCTCTGTGTCTTCGTGGTTGACCTGAACTTGCTCTGTAGATCAGGCTGACCTGACTCAGATTTCCCTTACCTTTGCTTCCCGAGTGCTGGGATTAAAGGCTTGTGCTATCACCACCTGGCTTCCCCCACTTCTGTTTTTTGACATAGGGTTCAGACTAGCTTGGAAGTCACTATGTATACCAAGCTGGTATCAAAAGCTCATGGCATCCCTCCTGCTTTGCCAGGCCCAGTGCTGGGATTATAGCTGCCACACCTGGCCCCATATAGCTTTTTTTTTTCTTCTTTTTTTCGGAGCTGAGGACCGAACCCAGGGCCTTGCACTTGCTAGGCAAGCGCTCTACCATTGAGCTAAATCCCCAACCCCATAGTTTTTAAATAGGAAAATGTGAAATAATGTGCTACCGAGTTTAAAAGCAAGGTGTCACAAAGTTATTAAAGTGTAGGCAGCTGCACTGTGTGGGCCCTCATCGGCTCTTTGAGTAGACATGTTTGAATAGTAGGTCCTGTTCAGCCCCCTTCCCCACTCTGCTTCTCCTGATCCCAGCTCAACCCCTACTTGGGTCAGGGACAAATGACTCTGTTTGGTCCCCAG
Seq C2 exon
GCACCAGGTGCAGCATGATGGCTCTCTGGTCATCAGCCGAGTGACTGTGGAAGATGGTGGCTTTTACACCTGTGTTGCTTTTAATGGGCATGACCGAGACCAGCGCTGGGTCCAGCTCAGAGTTCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009448:ENSRNOT00000012757:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.702 A=NA C2=0.182
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(49.4=87.2)
A:
NA
C2:
PF0767911=I-set=PD(49.4=93.2)
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:
CTACGTCTGGACCGGACTCAG
R:
TCTGAACTCTGAGCTGGACCC
Band lengths:
265-1815
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]