GgaINT0125026 @ galGal4
Intron Retention
Gene
ENSGALG00000008681 | NSMF
Description
NMDA receptor synaptonuclear signaling and neuronal migration factor [Source:HGNC Symbol;Acc:HGNC:29843]
Coordinates
chr17:1747019-1748929:+
Coord C1 exon
chr17:1747019-1747108
Coord A exon
chr17:1747109-1748807
Coord C2 exon
chr17:1748808-1748929
Length
1699 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
TGCACGCTGTGTTCTGACAGGCC
3' ss Score
8.39
Exon sequences
Seq C1 exon
CATTTGCCGAACGGCGTGAGAGGAGCTTCAGCAGGTCCTGGAGTGACCCGACTCCCATCAAAGCTGATTCCTTCCATGACTCTCGAGAAA
Seq A exon
GTGAGTTCTGAGTCCTTTGAGCTTCCTCCTGTGGCCAAACCCTCCAGCTGAGGTGTTGACTGGAGTCCCACTGGAGTAACTTCTCTGTTCCCTTTTGTCCCATTTGTTATCCTTTTAGTTCCATGAGATCTGAGCAGATAATACTCTGGGTTTATGCACCTGGTCATCTGTGTGTACCTGTATTTACAGGTAGAGCACAAGCACATCTAACCTCATGTTTTTGTGCAGCAGCCAAAGGACACCCTTTGAGAGTACAGCTCTCTTATGGCTCTCTGTTCTCACCATTCCTTGTTTGCCTGGGGGCAACACACTACCTGGAAGCACATCGGTCCAAGGTTGCATTCACCATAGAGGGGCAAACCTTCCCAGTTTCCTGTGCAAGAGCCCCTTCTGAGCTCTTCTGTAGCCTAGAATAATTCGGAGCAAAGCTGCAATGTTCCGTGAAACATAACTTTGATTTCCTATTTGTGCAGGCTTCACAGATGATAGCTTGGGGCGATCTGATCTTTGGGCTGCCAGGAATTCCTCTGGAAATCCTCAGTAATGCTACGGTGTTCCGCTTGTGGGGACCCAGGTGCTGTTGTGATAATTTACAGAAGGAAATGCCAGCATCTTCCCACTGTCTTTTTTTTTTTTTTTTTTTTTTGTAAAGAGAATGTCTGGTTCACCCAATTTTCATTTGAAATCCTGCAGGCAAGGGTTATGAGTTTGGTTATGAGTTTGCCCATGCTGACATGGGTTGTATTCATTACGTAAACTTCACTACTGAAATCAACTGACCTTTCAGGTAAGCATGAGGTCCGGCCCTCCTGGTTGGAGATCACACCGTACCAGGTTGCAGGGGGAGATGTGTGAAAGGCCAGGTTCAAAACATGACCCGATGGTTCCTTTGCAGTCTGATTCTTCCCTGCTCCCTCAGCTAACTCAGAAGCGAATGGAAAAGACATGGTTCACACAGATGTGTTTGGTGCTCCAGCACTGTCCAACGACACTTGGACATCCCAAAAGACACAAGTGGAGGCACCTCTGTTCTCTTTCCTCAGTCCCTGGCTTAAGGGAACCATCTTTATTTTTAACATTTAACGGTCAATTATATTCCTTCCAGATGTTTTTTTCCCCAGGAGGCATTGAAGGCCAACAGGTAAGGTGAATTTGGAGAGCAAATTCAAGTATACTGTGGAAATACCACTGTGTTTGCTACAGCCGTCCTCGCGCTCTGGGATTCTCTGCCAGGATCAATTTGACTAAGAAGGCAGAGTTTCTGTATAAGCACTGAGAAAACGTAGTCAGACCAGTAATTATTACAAGGAGACCAGCTTTGGAGTCTTTGGACTTTTGCTCATCAGCTTGGCAATGTTAAAGTGTAGAGAGTCTGTCTGCATTCCATCTCCTTCCCCATTTCTGAAATGACAGGGTGACTGTTGTGAATTAGCATCTAAAAGCTTAAACTTGGTGACTGTGAGAGTGATGAAATGTTATGTGATGTGTGGTATCAGACTCTGTGTGCACTCGTCGTTTGTCAAGAGAGTTTGTCTGTTTAGAGACGCCAGCCCCGACGTGTGGTGTCTGTCACTGTGCTGGAAGGAAGGAGGGCACAAGTCTCATGGCTTGTGGGGCTTCTTGCGAGGTAGCTGCCAGACAGGGCTGAGTGAAGAAGGCAAGCTGTTCTGCCCTTGTGATGCACGCTGTGTTCTGACAG
Seq C2 exon
GCCATGACCTTCAGGATTCCTGTGGCACTTTGGATGGTGACTTTGACTTGAACTGGGAAGCAGAAAAGGAGCTTGAAGCCATGGCGTGTGACGGAGAAGACTTTATTCCACCAAAAATAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008681:ENSGALT00000014129:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.323 A=NA C2=0.018
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACGGCGTGAGAGGAGCTT
R:
TTTTGGTGGAATAAAGTCTTCTCCGT
Band lengths:
198-1897
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]