GgaINT0124454 @ galGal4
Intron Retention
Gene
ENSGALG00000002375 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:HGNC:7881]
Coordinates
chr17:7835862-7837231:+
Coord C1 exon
chr17:7835862-7836290
Coord A exon
chr17:7836291-7837082
Coord C2 exon
chr17:7837083-7837231
Length
792 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
CATTGACTCTTCTCTCGCAGATC
3' ss Score
10.32
Exon sequences
Seq C1 exon
CCCTCTGTACGACCAGTACTGTAAGGACCACTTCTCAGATGGTCACTGTGACCAGGGCTGCAATAACTTTGAGTGTGAGTGGGACGGGCTGGACTGTGCAAACAACATGCCCGAGAAGCTGGCGGATGGCACGCTGGTGGTGGTGGTCCTCATCACCCCTGAGAACCTGAAGAACAATTCCTTCAATTTCCTGAGGGAGCTGAGCCGTGTGCTGCACACCAATGTAGTCTTCAAGAAGAACGCCAAGGGAGAGTACATGATCTTCCCATACTATGGCAACGAGGAGGAGCTGAAAAAGCACTACATCAAGAGGTCAACGGAGGACTGGGCAGATATGTCCAGTGCTGTCATCAACAAGGTGAAGAGCAGCCTCTACTCGCGGGCTGGCAGGAGGCAGAAGAGAGAGCTGGATCAGATGGACATCAGAGG
Seq A exon
GTAAGGGGCCTCTGTCACAGAGCAGGGTTGGTTTTGTGCCTTGATAATAATAACACAGAATCGCAGAACCATTAAGACTGGGACGGCCCTCTCAGATCCCCAACCTCAGTCTGTCCCACGGTGCCCTCTGACCACATCCCTCAGTGCCACATCTCCACTGTTCTGGAACACCTTCAGGGATGGTGGCTGCCCCGCTTCCCTGGGCAGCTGTGCCAGTGCATTACCACTCTTTTGGAGAAGAAATCTTTCCTAATACCCAACCTGAACCTCTGCACAGTGCTGCGGGGCTCCCACACTGGGTGTTGTTGGGCAGGGGGGCTGGCCCAGCTGATGTCTGCTCGCAGGAAGGCGTTGGGCTAAGCCTCAGGTTCTCCCTGGGAAATGCTTCCGAGAGCTTTGTTGTAAAACTCAATCGCTGCAGACTGTGTTTGGAGCTCTTTTGTATAAACATATAGATCTGACCTTCCCTCTCTGTGGACTCAATCAAAAGTCAACGAAACCAAAGGAGTTTGAGCAGTGAAACTGATGTGAAAGATCTTAAGGCTCCCAAACAGCCTTATTTACAATATTGTAGTGTCTGGGTAGTTTCAGAGCATGGTGCAGCAGGTTCCCTTGCATTCCTGTAGATAAGGAGTCAGGCTTTGCAGTGTTCATGGAGGCAGATCCAATAGACCACCAGTGTGAGCCCAGGGCTCGGGCCAAGGAGAAGAGACGAGATGGGCTCACACCTCCTGCTGCCCTGCAGGGTGAGTGATGGTGGCCCCTCACTTCCCATTGACTCTTCTCTCGCAG
Seq C2 exon
ATCCATCGTCTACTTGGAAATTGACAACAGGCAGTGCATCCAGTCGTCCTCCCAGTGCTTCCAGAGCGCAACCGATGTGGCGGCCTTCCTGGGGGCCTTGGCCTCCCTGGGCAACCTCAACATTCCCTACAAAATAGAGGCCGTCAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002375:ENSGALT00000003754:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006612=Notch=PD(82.5=22.9),PF068168=NOD=WD(100=39.6),PF076847=NODP=PU(4.8=2.1)
A:
NA
C2:
PF076847=NODP=FE(79.4=100)
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:
GGTCCTCATCACCCCTGAGAA
R:
CACTGGGAGGACGACTGGAT
Band lengths:
342-1134
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]