BtaINT0104035 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030247 | NSMF
Description
NMDA receptor synaptonuclear signaling and neuronal migration factor [Source:HGNC Symbol;Acc:HGNC:29843]
Coordinates
chr11:105679259-105680002:+
Coord C1 exon
chr11:105679259-105679348
Coord A exon
chr11:105679349-105679877
Coord C2 exon
chr11:105679878-105680002
Length
529 bp
Sequences
Splice sites
5' ss Seq
ACAGTAGGT
5' ss Score
5.67
3' ss Seq
TGGCACGTCCTGCCCTCCAGGTA
3' ss Score
8.61
Exon sequences
Seq C1 exon
CGTTCGCCGAGCGGCGCGAGCGGAGCTTCAGCCGGTCCTGGAGCGACCCCACCCCCATGAAAGCCGACACCTCTCACGACTCCCGAGACA
Seq A exon
GTAGGTGCCCGGCACCGCAGGCCGGCCCACCTTCCCCAGAGGCTCCCCTAGGCCCCCAGCCCCACGCTTCCAGCACCCAGATGGCTAGGCTTCTGCGCTTCCGCTGGACCTCGGTTTATTGGGCTGAGGGGGGCACTCTGACACCTCCAGTCTTCTGGGTAGGGGTTACTAAGGGCCAGGGTTCACTGGCTACCCTGCCTGGTGCCCCTAACGCCGGAAACCTGCAGTACCTGATTTCTCCTTGGCCCAGACGCCAGGCACACCGGGCTGGAGCTGACACTTGCACCTCGGCTCCCACTGGCCTTGCCCTAGGGCCCACAGCCTTCCCTGCCAGGCAGCCTCCAGCTGGTGGCAGCAGCCCGGCTTGCCCTCAGCTTGGCTCTCTTACCTGCCCTGGGTTTCTCACTGGCCTGGAGGGCCCTCTGGGACACGGCTTGCTGGCTCTGTCCCCTGCCCATCTCTGGGGTTGCAGCCAGGGCGGGTGGTACTCCAGATGGTCCTCAGCCTGGTGGCACGTCCTGCCCTCCAG
Seq C2 exon
GTAGTGACCTGCAGAGCTCCCATTGCACCCTGGGCGAGGCTTTCGAGGACCTGGACTGGGAGACTGAGAAGGGCCTGGAGGCTGTAGCCTGTGACACTGAGGGCTTCGTGCCACCCAAGGTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030247:ENSBTAT00000016087:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.774 A=NA C2=0.095
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF142521=DUF4347=PU(1.4=4.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGCTTCAGCCGGTCCT
R:
ATGACCTTGGGTGGCACGAAG
Band lengths:
193-722
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development