RnoINT0069116 @ rn6
Intron Retention
Gene
ENSRNOG00000018870 | Hapln2
Description
hyaluronan and proteoglycan link protein 2 [Source:RGD Symbol;Acc:621854]
Coordinates
chr2:187396349-187397374:-
Coord C1 exon
chr2:187397192-187397374
Coord A exon
chr2:187396805-187397191
Coord C2 exon
chr2:187396349-187396804
Length
387 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCACCCGCTCACATTCCCAGGCC
3' ss Score
7.55
Exon sequences
Seq C1 exon
CGTGGACCGAGGGGCTGGACTGGTGCAACGCCGGTTGGTTGCTCGAGGGCTCCGTGCGCTACCCTGTGCTCAACGCGCGGGCTCCATGCGGCGGCCACGGGCGGCCAGGCATCCGCAGCTACGGGCCCCGCGACCGCAGCCGCGACCGCTACGACGCCTTCTGCTTCACCTCGGCCCTGGCAG
Seq A exon
GTGAGCCAACTGCTGGCAGGCGGCTCTGCCTTCAGGAAGGGCTGTGCAGTGTCTGGGCCAGGAAAGAGGACTCCCGGGCCGGGAGAAAGGACCCAGGAGGTGGCAGAAGCTCGACTTGTTGGCGGAGCAGGGTCTAGTTTGCTCCCAGTGTCAGGGGCCGGGCCTGGAGGAAGAACGGGGCGGGGCCGGGGGCGGGGCCCAGTGTCAGAAGCCAGGCAGAGAGAAAGGGTGTGGGCGGGGTCTGGTGTCAGGGCGATCGCGTCCTAGACAACCTTCCTCCGCACGGTCCTGGGAGGGGTTCTCGTGTTGTCATTTCTGGAGCTCCGCGGCCAGGTCCCTGTCCCAGGCCAGCTGCTCTGGACGCAGCTCACCCGCTCACATTCCCAG
Seq C2 exon
GCCAGGTCTTCTTCGTGCCTGGACGGCTGACGTTGTCCGAAGCCCACGCGGCTTGCCGGCGGCGCGGAGCTGTAGTAGCCAAGGTCGGGCACCTCTACGCCGCCTGGAAGTTCTCGGGGCTGGATCGGTGCGACGGAGGCTGGCTGGCGGACGGCAGCGTTCGCTTCCCCATCACCACGCCGCGGCCGCGCTGCGGGGGTCTCCCTGACCCCGGGGTGCGCAGCTTCGGCTTTCCCCGGCCCCAGCAGGCGGCCTACGGGACCTACTGCTATGCCGAAAAGTAGCAGTGCATTGCCCTGCCACGCGCGACAGAGTGGCGGGTCCCCTCTGGACAGACGAGGGCTGAGCCCCCCTCACCTGCCTTCCCAGGCAGCGAGATGCTCTGGGCTCCTGGGTAAAGGGGCTTCCTGGGCATTAACTGACCAATAAAATAACATGGCACCTTCTTTGTTCGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018870:ENSRNOT00000025624:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.065 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0019312=Xlink=PD(57.9=88.7),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=95.8)
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:
CAGGCATCCGCAGCTACG
R:
GGCATAGCAGTAGGTCCCGTA
Band lengths:
353-740
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]