RnoALTD0002234-2/4 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000020205 | Agrn
Description
agrin [Source:RGD Symbol;Acc:2067]
Coordinates
chr5:173610373-173611202:-
Coord C1 exon
chr5:173611011-173611202
Coord A exon
chr5:173610854-173611010
Coord C2 exon
chr5:173610373-173610420
Length
157 bp
Sequences
Splice sites
5' ss Seq
ACTGTACGT
5' ss Score
6.33
3' ss Seq
ACCTAACTTTTCCTCCCCAGACA
3' ss Score
9.65
Exon sequences
Seq C1 exon
TGCTTATCTCCTACCATGAACCTGGAGGGCTGGGGAGAGGACCTGGTGCTCCCCTAGCCATAACTGGCTAAACTTTGAGATCACAGCTGCATCTGCTGCTCCAGAGCACCCAGCATGGGGGGAGTAGCTCCGAAGAGGCCTAAGGGCACTCCATAAGAACTCCCACACACACCCAGGAATTGGGCTCGAGCT
Seq A exon
GTATGTATCATGCCTCCTCTGCCACTGGAACACAGACCCAGGCAGGAGCCTGGTGCCTCCATGCTGGTTCGATACTTCATGATCCCCTGCAACATCTGCTTGATCCTGTTGGCCACTTCCACATTGGGCTTTGCGGTTCTGCTTTTCCTCAGCAACT
Seq C2 exon
ACAAACCTGGAATCCACTTCACACCAGCGCCTCCTACGCCTCCTGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020205-6-2,7-2,8-2,9-2-2/4
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.180 A=NA C2=0.047
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0314610=NtA=PD(5.9=11.8)
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:
TCTCCTACCATGAACCTGGAGG
R:
CATCAGGAGGCGTAGGAGGC
Band lengths:
234-391
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]