DreINT0106768 @ danRer10
Intron Retention
Gene
ENSDARG00000060025 | nsmfa
Description
NMDA receptor synaptonuclear signaling and neuronal migration factor a [Source:ZFIN;Acc:ZDB-GENE-091204-32]
Coordinates
chr21:13396375-13397454:-
Coord C1 exon
chr21:13397396-13397454
Coord A exon
chr21:13397164-13397395
Coord C2 exon
chr21:13396375-13397163
Length
232 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGA
5' ss Score
7.41
3' ss Seq
TCCTAATGTTTGATTTGAAGATC
3' ss Score
6.09
Exon sequences
Seq C1 exon
AGCAGCTCGTGCATTTGGAGAGTACCTTCACACCCATCCTGAGAACTGCAACGGATCAG
Seq A exon
GTCAGACATCTCCATTCCTCTTTCTTTCTGCTGTTAATCTTTGTACTTCTTATTTCTGATCCACCTATAGATTGTGAATTTTGTTAGACTCCAGGCGCATTCATGTTTCATGACGAACTGTGCCATTCCTTAACGTAGCATTTGTTACCTCATTCGTCTTTTTTCTCTGTGCATCTCTCTTGTTCTTCTTTCTTTCTTTCTCTCTGCATCTGTCCTAATGTTTGATTTGAAG
Seq C2 exon
ATCACTTACTGTCTGACACCCTCGTTGGCCACGACTCTGACTCCCCAGACAGCCTGTGTGCTCAGAACAACAACCACAGCTGTACCCTCCAGGGCTCCCCCATCAGCACCGACGCCAGCCTGATCAACCCTGCCCTGGGTCTTCTGGAACCACCACCCCCTACAACATCCTCCAAGAGCCGGTTATCCCTAGAGCGCAGCTTTTCAGCAGAGGAGGACCAGCAGAAGTGTGTGGAGTGTGCCCTGCAGCCTGCTCGAGTCTACACCATCACCGGAGAGAGCGGAATGCTGGGAACCAGTCGGGGAAGCAAAGAGAATCTGGAGCTTGAGGTCTTGAAAGAGGCTCTCTCCCAGCCCTCGACATCATCCAACACGTCATCTCCAACCCAGCGACACCACCACCATGGAGGCGGAGGTGGAGGCGGAAACCATCATCACAGCAATCACCATCATTCCAACCACCATCATGCCAACACCAGCGGTAGCAGTGGAAATAGCGGATCAACCCCCCAGAATATCTCTGGAGCAGGAACGTCACACCATCACCACGTGGTGTCCCATCACCATCACCACCTTTCCCAGCCACTCCAGAGTTCAGTCAGCGCACACAATCTTCGTGGCTGGGGAGAGGGAAAGGAATGCGGCCTGGCATGTGAGAGTTGTCCTGGGGCTCCATCACGCAGCCAGGGCTCCCTGGACCTGGAAAGCAGCACCCGAGAGGCAGGCAAGCAGCGCCGGCCCCCTCTAGAGCGGATGTGCAGTGTGGACCGCGTGACTGGGCTGGAGCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060025:ENSDART00000139568:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.238 A=NA C2=0.830
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion 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:
CAGCTCGTGCATTTGGAGAGT
R:
CTCCACACACTTCTGCTGGTC
Band lengths:
293-525
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]