DreALTD0013007-3/3 @ danRer10
Alternative 5'ss
Gene
ENSDARG00000060025 | nsmfa
Description
NMDA receptor synaptonuclear signaling and neuronal migration factor a [Source:ZFIN;Acc:ZDB-GENE-091204-32]
Coordinates
chr21:13394282-13397115:-
Coord C1 exon
chr21:13396445-13397115
Coord A exon
chr21:13396375-13396444
Coord C2 exon
chr21:13394282-13394348
Length
70 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
TTATGTTTGTTTCTAACCAGACG
3' ss Score
8.08
Exon sequences
Seq C1 exon
AGCAGAAGTGTGTGGAGTGTGCCCTGCAGCCTGCTCGAGTCTACACCATCACCGGAGAGAGCGGAATGCTGGGAACCAGTCGGGGAAGCAAAGAGAATCTGGAGCTTGAGGTCTTGAAAGAGGCTCTCTCCCAGCCCTCGACATCATCCAACACGTCATCTCCAACCCAGCGACACCACCACCATGGAGGCGGAGGTGGAGGCGGAAACCATCATCACAGCAATCACCATCATTCCAACCACCATCATGCCAACACCAGCGGTAGCAGTGGAAATAGCGGATCAACCCCCCAGAATATCTCTGGAGCAGGAACGTCACACCATCACCACGTGGTGTCCCATCACCATCACCACCTTTCCCAGCCACTCCAGAGTTCAGTCAGCGCACACAATCTTCGTGGCTGGGGAGAGGGAAAGGAATGCGGCCTGGCATGTGAGAGTTGTCCTGGGGCTCCATCACGCAGCCAGGGCTCCCTGGACCTGGAAAGCAGCACCCGAGAG
Seq A exon
GCAGGCAAGCAGCGCCGGCCCCCTCTAGAGCGGATGTGCAGTGTGGACCGCGTGACTGGGCTGGAGCGAG
Seq C2 exon
ACGATAACAGTTGGTTCCCTAAAGAGAACATGTTCAGCTTTCAGACTGCTACCACAACTATGCAGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060025-3-5,4-5,5-5-3/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.830 A=NA C2=0.435
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGGGGAGAGGGAAAGGAAT
R:
GCCTGCATAGTTGTGGTAGCA
Band lengths:
168-238
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]