RnoINT0069115 @ rn6
Intron Retention
Gene
ENSRNOG00000018870 | Hapln2
Description
hyaluronan and proteoglycan link protein 2 [Source:RGD Symbol;Acc:621854]
Coordinates
chr2:187397192-187397623:-
Coord C1 exon
chr2:187397507-187397623
Coord A exon
chr2:187397375-187397506
Coord C2 exon
chr2:187397192-187397374
Length
132 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGC
5' ss Score
7.75
3' ss Seq
TCCACCCTCTCCTCCGCCAGCGT
3' ss Score
7.43
Exon sequences
Seq C1 exon
GTGTGGTGTTTCCGTACCAACCCAGCCGGGGCCGCTACCAGTTCAATTACTTCGAGGCGAAGCGGGCGTGTGAGGAGCAGGACGGACGCCTGGCCACTTACAGCCAACTCTACCAGG
Seq A exon
GTGAGCGGCGGCCTCCCTTCCGGCTGGCGTCCCCCCGCCCCGCGGCTGCATATAGGCCCGGGCGCTCTTGCGGGGAGCTAGAGTCTGGCTTGCGCCGGTGACTCCTGTCCTCTCCACCCTCTCCTCCGCCAG
Seq C2 exon
CGTGGACCGAGGGGCTGGACTGGTGCAACGCCGGTTGGTTGCTCGAGGGCTCCGTGCGCTACCCTGTGCTCAACGCGCGGGCTCCATGCGGCGGCCACGGGCGGCCAGGCATCCGCAGCTACGGGCCCCGCGACCGCAGCCGCGACCGCTACGACGCCTTCTGCTTCACCTCGGCCCTGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018870:ENSRNOT00000025624:5
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=0.065
Domain overlap (PFAM):
C1:
PF0019312=Xlink=PU(41.1=97.5)
A:
NA
C2:
PF0019312=Xlink=PD(57.9=88.7),PF0019312=Xlink=PU(0.1=0.0)
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:
GGGCCGCTACCAGTTCAATTA
R:
AGAAGGCGTCGTAGCGGTC
Band lengths:
251-383
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]