BtaINT0104031 @ bosTau6
Intron Retention
Gene
ENSBTAG00000030247 | NSMF
Description
NMDA receptor synaptonuclear signaling and neuronal migration factor [Source:HGNC Symbol;Acc:HGNC:29843]
Coordinates
chr11:105675130-105676850:+
Coord C1 exon
chr11:105675130-105675630
Coord A exon
chr11:105675631-105676774
Coord C2 exon
chr11:105676775-105676850
Length
1144 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
GCCTCCTTGGCCTCTTCCAGATG
3' ss Score
9.01
Exon sequences
Seq C1 exon
ACCACCTGCTGGCTGACGCCTGCTCTGGCCACGACGGGTCCCCCGAGATGCAGCCGGCCCCTCAGAACAAGCGCCGCCTTTCCCTCATCTCCAACGGGCGATATGAGGGCAGCCTTCCGGAGGAGGCTGCCAGCGGGAAGCCGGCTGGTGAGGGCCCCCAGCCCCGCGTGTACACCATCTCAGGGGAGCCGGCCCTGCTGCCCGGCCCGGAGGCCGAGGCCATCGAGCTGGCTGTGGTGAAGGGGCGGCGGCAACGGGAGCAGCACCCCCACCACCACAGCCAGCCCCTGCGCGCCAGCCCGGGCGGCAGTCACGAGGACGTCAGCAGGCCCTGCCAGAGCTGGGCGGGCAGCCGCCAGGGCTCCAAGGAGTGCCCCGGATGCGCCCAGCTCGCCCCCAGCCCCTCCCCTCAGGCCTTTGGGGTAGACCAGCCGCCTCTGCCTGAGGCTCCCGGCCGCCGCAAGAAGCTGGAGAGGATGTACAGCGTTGACCGAGTGTCTG
Seq A exon
GTGAGGGGCTGGGCGGGGGCCCGGGCAGCCCCCTCTGCAGCAGCAAGCGCCAGGAGGCCTGGACAGTGCGGGTGCCCCGGTCACCGCCCGCAGGTGGCGTCCTGCCACCACACCCCACGCCCAGCCAGGCTTCATGGTTGGCTTCAGGCTTGCCAGCACCAAGTCATGGCAGGCTTGCTTCCCCAGCACGGGGCTGGGAGGGTCTTAAGGGTGGAATGGGCAGCAAGCCTGGTTGAGTGGAAAGGTGGGGCTGCCTTCTGGGAGTGCTGGGGGACAGTCCCTCCCCTGGCACCCACCCAGTGGGACTCCTGCTCACCAAGGGGGCCTGGCCAGCTAGTGGGGCCCCCCACCAGAATTGTCGAGCAATGCGCATGGCTGAGGAGCCCTGGAGGCCTGCTGTCAGGAAGAAGCTGCCTGGGACATTCAGGTGGTCCCCATGCTTCTGGGCTCCGAGCCCATCACTTCCGGAAGAGCAGAATTCTACCTGGCAGACCCGCCGTGTGCTCTCCGGGCACCTCTTGAGCCTCCAAATCCGCAGTCCAGCGGGGCATCAGGGCACAGGCCAGGGGTGCAGACATCGCCAGGTCCTCGTGCTCCTCTGAGGAACACAGGCCAGGTTCTGGAATGCAGTCAGGGAAGAGAATAGAGTGGCACCCTGTCTGGTGGCTATAAGGCCTCTGGGAAGGGTCAATCTCCCTGCCTGGTGAGGGCCTCCACCAGGAAGGTCTGAGAGAGGGAAGGGCCGACCATGTGGACTCCAGAGTGTCTGGGCGGCAGAGAAAGCCCTGGAGCCCCAGGAGAGGCAGCCACGGTCCCTGCCCCGCCCCTCCGGCTTGAAGGCGACGAGTCAGTGCTTTTCCTGGGTGCCTTGGAGGCCGGCTGTGCTTTCCGGGGAACACGTGTCCGCTGTGGGCAGCAGGGGGAGAGCCAAGTGAAGACGAGCGTCACGAAGCCGCTGAGCTGTCGCGGCTTGAACAGCTGAGCGGGCCTCAGAGCCTGCTGGCCCGGTGCCAGGCCCCGCCCCCCTACCCCGGGATAGGTCTAGGGAATCCTGTGCTCAGGAACACCCCCAGCCCTGGGCAGGTGGGAAAGGGCTCAGGAACCCCTAAGCCACCCTAGTCACTGCCTCCTTGGCCTCTTCCAG
Seq C2 exon
ATGACGTCCCCATCCGTACCTGGTTCCCCAAGGAAAACCTCTTCAGTTTCCAGACAGCAACCACAACTATGCAAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000030247:ENSBTAT00000016087:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.970 A=NA C2=0.038
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTACACCATCTCAGGGGAGC
R:
AACCAGGTACGGATGGGGAC
Band lengths:
358-1502
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development