RnoALTD0013371-2/3 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000022321 | Hapln3
Description
hyaluronan and proteoglycan link protein 3 [Source:RGD Symbol;Acc:1308098]
Coordinates
chr1:140828451-140832030:-
Coord C1 exon
chr1:140831906-140832030
Coord A exon
chr1:140831662-140831905
Coord C2 exon
chr1:140828451-140828753
Length
244 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGG
5' ss Score
5.5
3' ss Seq
CTTCCTTCCTCCCTTTCTAGGTG
3' ss Score
14.87
Exon sequences
Seq C1 exon
GCCTATTCAATGGCGTGAAGTTAGTGGTGGAGACCACCGAGGAGTCGTTGTTCAGTCACCAAGGAGCCAGTGTGACCCTGCCCTGCCACTACCACTATGAGCCAGCCCTGGCATCTCCGAGACAT
Seq A exon
GTGCGTATTAAGTGGTGGAAGTTGTCAGAGAATGGAACCCCGGAGCAAGACGTGCTGGTGGCCATCGGGCAGAGGCACCGCTCCTTTGGGGACTACCAAGGGCGAGTTCAATTGAGGCAGGACAAGGAGCAGGAGGTCTCACTGGAGCTTCGAGACCTGCGGCTGGAGGACTCTGGGCGCTACCGCTGTGAGGTCATTGACGGTCTGGAAGATGAGAGTGGCCTGGTAGAGCTGGAGCTGCGGG
Seq C2 exon
GTGTGGTTTTTCCCTACCAGCCCCGAGAAGGGCGCTACCAGCTCAATTTCCATGAGGCCCAACAGGTCTGCCAGGAGCAGGATGCTGTGGTAGCCACTTTTGAGCAGCTTTTCCGAGCGTGGGAGGAAGGCCTAGACTGGTGCAATGCAGGCTGGCTACAGGATGCCTCCGTGCAGTACCCTATAGTGCTGCCCCGGCAGCCCTGTGGAGGCCTGGGTCTGGCACCTGGGGTTCGCAGCTACGGCCAGCGCCATCACCGCCTGCATCGCTATGACGTGTTCTGCTTTGCTGCTGCCCTCAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000022321-3-3,4-3,5-3-2/3
Average complexity
Alt5
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:
PF0768612=V-set=WD(100=92.7),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=WD(100=94.1),PF0019312=Xlink=PU(0.1=0.0)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
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:
GGCGTGAAGTTAGTGGTGGAG
R:
TATAGGGTACTGCACGGAGGC
Band lengths:
299-543
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]