RnoALTA0033547-2/3 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000008239 | Repin1
Description
replication initiator 1 [Source:RGD Symbol;Acc:1549707]
Coordinates
chr4:78233332-78234836:+
Coord C1 exon
chr4:78233332-78233525
Coord A exon
chr4:78234733-78234735
Coord C2 exon
chr4:78234736-78234836
Length
3 bp
Sequences
Splice sites
5' ss Seq
AGGGTAGAG
5' ss Score
0.88
3' ss Seq
TTGTGCTTTTCCATCCTCAGCAG
3' ss Score
7.56
Exon sequences
Seq C1 exon
TAAGGCTGACCTCTCAGCAGTTAGAGGTCTGAGCTCTGCCATGGGGATAGGGATGTCTTTATTGCTACAGTTTTCTCTGACATCCGGGGGCTACCGAAGTGTGGGCCGAAGCAGGCGCTGCAGCAGAAGTATCCCCAGGAACATCCCCAGAAGGAGCTGGAAAAAGCCTCATCCCCAGCTCTGCAGTCTTCAGG
Seq A exon
CAG
Seq C2 exon
AGGAAGAACCGATGCTGGAACGGCGCTGCAGGGGCCCCACGGCCATGGGCCCAGCCCATCCCTGGCTTTTTTCTGGGCCCTCCCAGGAGTCCTCCCAGCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008239-1-4,1-3,1-1-2/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.192 A=NA C2=0.250
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF134651=zf-H2C2_2=WD(100=4.9),PF0009621=zf-C2H2=WD(100=4.2),PF134651=zf-H2C2_2=WD(100=4.7),PF134651=zf-H2C2_2=WD(100=4.7),PF134651=zf-H2C2_2=WD(100=4.5),PF134651=zf-H2C2_2=WD(100=4.7),PF134651=zf-H2C2_2=WD(100=4.7),PF134651=zf-H2C2_2=WD(100=4.7),PF134651=zf-H2C2_2=WD(100=4.7),PF138941=zf-C2H2_4=WD(100=4.3)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCAGCAGAAGTATCCCCAG
R:
CGTTCCAGCATCGGTTCTTCC
Band lengths:
99-102
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]