MmuINT0109746 @ mm9
Intron Retention
Gene
ENSMUSG00000026923 | Notch1
Description
Notch gene homolog 1 (Drosophila) [Source:MGI Symbol;Acc:MGI:97363]
Coordinates
chr2:26321987-26323550:-
Coord C1 exon
chr2:26323149-26323550
Coord A exon
chr2:26322136-26323148
Coord C2 exon
chr2:26321987-26322135
Length
1013 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TGTGCCATGTGTGTTCTCAGCTC
3' ss Score
8
Exon sequences
Seq C1 exon
CCCCCTGTATGACCAGTACTGCAAGGACCACTTCAGTGATGGCCACTGCGACCAGGGCTGTAACAGTGCCGAATGTGAGTGGGATGGCCTAGACTGTGCTGAGCATGTACCCGAGCGGCTGGCAGCCGGCACCCTGGTGCTGGTGGTGCTGCTTCCACCCGACCAGCTACGGAACAACTCCTTCCACTTTCTGCGGGAGCTCAGCCACGTGCTGCACACCAACGTGGTCTTCAAGCGTGATGCGCAAGGCCAGCAGATGATCTTCCCGTACTATGGCCACGAGGAAGAGCTGCGCAAGCACCCAATCAAGCGCTCTACAGTGGGTTGGGCCACCTCTTCACTGCTTCCTGGTACCAGTGGTGGGCGCCAGCGCAGGGAGCTGGACCCCATGGACATCCGTGG
Seq A exon
GTGAGTGCTCCAGCTCCTGCTGTTGTGGGCTGTTTCCCAGTGTGTCCCTGGGTTCTCTAACCAGCTTAACCCTGGAGGTGTAACCTCAGGGGAGGTAGTATTCACCTTATTTTATAGTCAGAAAGCACCTGGGATGAAGAGGGCATCCCTCTGATGAGGACTTGGCAGGCCTCAGGGTTTGCCCAGATGTGATTTTCAGGCCCCACTGTGTACCAGGTGTTGGAGACCAAGCTGATTAAAGCCTCCAGGGTGTCCCCTGGGGCTAAGTCATCCTAGACCAATCCTGACCCTCAGTCACTACAGCCCTTATCCCTACTACAGAGGAGGCAGTGAGGGGTACAGAAGGGCACTGTTGCTGAGCCTGGAAGGCTGAGGAGCCGAGGGAGGCACAAATAAGAGCATCTCCTGGATGCTGCACAGAGCCATCTGGGGATGGGCAGGGAAGCACCAGCCAGGCATTTGGAGGTTCCAGGAGCCTTCGCTGTTGGGCATCTGCCTGGTGGCACCTCAGTGTCTCCTGACCCCAGTGGTTCCTGGTCCTGGTTTTCTTGTCGTGGGACTGTGGTGAAGGTCAGAAATTAATTGTTTCCTGGAGGCTGTTAGAATCCTGTTTCTGAGAGGCCAGTGACTGAGAGTTGGTGACTTGGCTGGCATGAGAGAGCTGACTCTCTGGCATCTGAGCCTGCTGTCACCTCAAGCTACACCATAGGGAGTCACAACTGCATCCTTGCAGTTCTGTGGGGCCCCAGGCACTGCTCTCAAGAGGGCATTGGATGCCTAAAGACTATTCTTTGAAGTAAGGAAAAGGGGTGCTGTGCACCTAAGGGGCAAGGCTAGACAGTGGAATGACCCCCGCTGAGTGCTAAACACTGGGGCAGCAGGGAGAGTGTCCCATTGCGGGGCTGTCGTCTGATAAGCCCTGTGGGTCAGGGTGATGGGCTAGGGAGTCAGAGCTGGTGTGTAGGCAGTGTACTGGGGTGTATCTAATCTCACTGTGCCATGTGTGTTCTCAG
Seq C2 exon
CTCCATTGTCTACCTGGAGATCGACAACCGGCAATGTGTGCAGTCATCCTCGCAGTGCTTCCAGAGTGCCACCGATGTGGCTGCCTTCCTAGGTGCTCTTGCGTCACTTGGCAGCCTCAATATTCCTTACAAGATTGAGGCCGTGAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026923-Notch1:NM_008714:26
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.033 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006612=Notch=PD(84.6=24.4),PF068168=NOD=WD(100=42.2),PF076847=NODP=PU(4.8=2.2)
A:
NA
C2:
PF076847=NODP=FE(79.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACTGTGCTGAGCATGTACCC
R:
ACATTGCCGGTTGTCGATCTC
Band lengths:
348-1361
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: