RnoALTA0017596-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000016659 | Habp2
Description
hyaluronan binding protein 2 [Source:RGD Symbol;Acc:1302979]
Coordinates
chr1:277095078-277095788:+
Coord C1 exon
chr1:277095078-277095197
Coord A exon
chr1:277095617-277095723
Coord C2 exon
chr1:277095724-277095788
Length
107 bp
Sequences
Splice sites
5' ss Seq
TAGGTATGA
5' ss Score
6.99
3' ss Seq
GGCGGCCTGCTCTCTCCGAGGTC
3' ss Score
-0.43
Exon sequences
Seq C1 exon
TGCTTCCGGTATGCAGACCAAATCCCTGCCAGAATGGCGGGGTCTGTTCCCGACACAGACGGAGGTCCAGGTTTAGCTGCGCCTGTCCAGACCAGTATAAGGGGAGATTCTGTGAAATAG
Seq A exon
GTCCGGACGACTGTTATGTCGGTGATGGCTACTCTTACCGAGGCAAAGTGAGTAGGACAGTCAACCAGAACCCATGCCTTTACTGGAACTCCCACCTCCTCTTGCAG
Seq C2 exon
GAGAATTACAACATGTTTATGGAGGATGCCGAGACCCATGGGATCGCAGATCACAACTTCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016659-5-7,5-6-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=80.5)
A:
NA
C2:
PF0005113=Kringle=PU(63.9=91.4)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTCCGGTATGCAGACCAAA
R:
AAGTTGTGATCTGCGATCCCA
Band lengths:
178-285
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]