RnoINT0107082 @ rn6
Intron Retention
Gene
ENSRNOG00000009448 | Papln
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:RGD Symbol;Acc:1311176]
Coordinates
chr6:107259322-107260550:+
Coord C1 exon
chr6:107259322-107259448
Coord A exon
chr6:107259449-107260342
Coord C2 exon
chr6:107260343-107260550
Length
894 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGG
5' ss Score
7.93
3' ss Seq
CCCTTTTTCTTTTTTGTCAGCTG
3' ss Score
8.79
Exon sequences
Seq C1 exon
GTCACCAGTCCCGCCTGGTATTCTGCACCATCGACAACGAGGCCTATCCGGACCACATGTGCCAACACCAGCCTCGGCCAGCCCACCGACGTTCATGTAACACTCACCCTTGTCCAAAGACCAAGCG
Seq A exon
GTGAGGCCTTGCCAATCCCTTCCACCTTTGGTAGAGCCCAGGTTGGGTGGGAAGGGAGGGGAAAGCCCTAAACTGTTTTAGGCACAGGGTGAAGGTTGGGGGACAGGGTTCCTCACATCAGGTGGCAACTGTCACTGAGGGGGGCACAGGGACTGAACACGAGACCCAGAACAGTTCTCTCCATTCATGCGATTCCTTGCAGTACTCAGAATGCCCAGTCTGGGAACAGGAGGATTTGGGGACAGTGTCAGAGGTCCCTGTCTGAGGCAACAGGGGGCTCAAGCAGAAGCCTAGGGGTAAGGCAGGAATTTGGCGAAAGGGCCAGTAGACTTTGGCAAATACCTTTGTTCGTGTACAAAGGATCTCTTTCCTGCACCGGCCTGGAGCGTGGCGCTATGGTGGGGCCCAGCATGTGTGTGGGAACAGGTAATCCGTGGGCCAGGGGGTTCCTGCAGGGCTGGTGTTGGTCCCCTCACCCTCCTGGCCTGGTGAGATGGTGGTGGGCTTGGCTTTGCATGGTATGTTTGGAGTTTCCCTTTCTTCTTGGTCCTTGTACCCCCAGCCAGGCAGGGCTTCTCCGCATACAGGGAGAACAGCCTTTCTGGAGATCACCTCACACAGGCTAGCAACCCACAGAGTCTGGCTGGGGTGCTGGGACCCAGTGAAAAGGAGAAAGGGAAAGTCGGGGTACAGACAGGAAGTCTGAGGGGCAGCAACCAGGTTATAGAGACCCTCCCGGGGCCACAGGAGATGCCTAGGAGGCCTGGCTGGTGGTCTCTCTACAGAGTTCTTGGGAGGGTTGGGATGGACCCTCGATGCACTCTGCGTTGGGGAGCTGCAGCCTCCTGGGCTAGTCTTAACTGTCCCCTCCACCCCCTTTTTCTTTTTTGTCAG
Seq C2 exon
CTGGAAAGTAGGACCATGGACGCCCTGCTCAGTCTCCTGTGGGGGTGGATTCCAGTCTCGCTCTGTCTACTGCGTGTCCTCAGATGGCACTGGTGGCCAGGAAGCTGCTGAGGAGACCCAGTGTGCTGGCCTAGCTGGGAAACCCCCTACCACACAGGCATGCAACCTGCAGCGCTGTGCAGTCTGGAGCGTGGAGCCCTGGGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009448:ENSRNOT00000012757:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.093 A=NA C2=0.076
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009014=TSP_1=WD(100=82.9),PF0009014=TSP_1=PU(13.0=10.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGTCCCGCCTGGTATTCT
R:
CTCTCCCCAGGGCTCCAC
Band lengths:
331-1225
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]