GgaINT0124453 @ galGal4
Intron Retention
Gene
ENSGALG00000002375 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:HGNC:7881]
Coordinates
chr17:7834532-7836290:+
Coord C1 exon
chr17:7834532-7835103
Coord A exon
chr17:7835104-7835861
Coord C2 exon
chr17:7835862-7836290
Length
758 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
CTTTCTTCCCTTCTGCCCAGCCC
3' ss Score
8.23
Exon sequences
Seq C1 exon
GGCTTTGTGGGTGCCACCTGCGAGAACGACTCCCACACCTGCGGGACCCTGCACTGCCTGAACGGTGGCACCTGCATCTCCATGCACAAGAGCTCCAAGTGTGTGTGCGCAGCGGCCTTCACGGGCCCCGAGTGCCAATACCCGGCCAGCAGCCCCTGCATCTCCAACCCCTGCTACAACGGGGGCACCTGCGAGTTCCTCAGCGACGCCTCCCCTTACTACCACTGCAACTGCCCCGCCAACTTCAACGGCCTCAACTGCCACATCCTCGACTTTGATTTCCAAGGCGGCTTCGGGCAGGACATCATCCCACCCAAAATCGAGGAGAAGTGTGAGATCGCCGTTTGTGCGAGCTATGCTGGCAATAAGATCTGTGATGGGAAGTGCAACAACCACGCCTGCGGCTGGGACGGCGGCGACTGCTCGCTCAATTTCAACGACCCCTGGAAGAACTGCTCACAGTCACTGCAGTGCTGGAAGTACTTCAATGATGGCAAGTGTGACTCGCAGTGCAACAACGCGGGCTGCCTGTATGATGGGTTTGACTGCCAGAAGTACGAGGGGCAGTGCAA
Seq A exon
GTAAGTGACTCGTTGGTCCTCTTGCTTTAAAGCCGTGAGCGCTGCAGTCCTCTGGCGGGGTCTTCATTCTCTTCTCCTGCATGTAGGGCTGCATCTCAAGTCCCCATAGTTCTCCCTGGTCCTACAGAGTTCTGTGCACATTTGGGAGCTCTCTCTGTTTGGCTTTGCTGCCCTGACCTGCATCGTGCCACAAATGTGCATTTTGTGACCAGCAGTAGTGGCACAGTGAGGTTCAGTGTAGGGAAGATGAAGCAGGAAGCATGGTGATGTGAGAATCCAGGCACGTCGCAGGCATTGTCTTTGACAACAGCGGGGACTTGTCCAGGAATCTGGGAGCAAATTCTAATCTGAATAACTATTTTGTGTCCTCATGTCTTCTCTGGGTCTCAGCAATTTGCCCCTTGCATCTAAAATGTGACTTGTAATGTAGCTCACAGCACTTCTCCCTGTTCTCTGGCATCTAGACTGTGACTTAGGACACAACAGCTGCTATCCTTCACCCCTTCGATGAGCACTTTGCAGTGCTCATGCATGGCACAATTGCCTTCCATGTCAACTGGTCCCATATCCATTAAGATAAATAATATTTACACAAAAGAGAGCTCTTTGGGAAGCACAGACTATTTTCTTAGCAATAATCGTAGAATCATAAAATCATTAAAGCTTGACTACTAAGATCATTTAGTCCAACCGTTGACCCGTAGCACGCACAGCACCTGCTCTAATTCATTCCTCTGTCTTTCTTCCCTTCTGCCCAG
Seq C2 exon
CCCTCTGTACGACCAGTACTGTAAGGACCACTTCTCAGATGGTCACTGTGACCAGGGCTGCAATAACTTTGAGTGTGAGTGGGACGGGCTGGACTGTGCAAACAACATGCCCGAGAAGCTGGCGGATGGCACGCTGGTGGTGGTGGTCCTCATCACCCCTGAGAACCTGAAGAACAATTCCTTCAATTTCCTGAGGGAGCTGAGCCGTGTGCTGCACACCAATGTAGTCTTCAAGAAGAACGCCAAGGGAGAGTACATGATCTTCCCATACTATGGCAACGAGGAGGAGCTGAAAAAGCACTACATCAAGAGGTCAACGGAGGACTGGGCAGATATGTCCAGTGCTGTCATCAACAAGGTGAAGAGCAGCCTCTACTCGCGGGCTGGCAGGAGGCAGAAGAGAGAGCTGGATCAGATGGACATCAGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002375:ENSGALT00000003754:24
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:
PF0000822=EGF=PD(14.7=2.6),PF0000822=EGF=WD(100=17.8),PF0006612=Notch=WD(100=19.4),PF0006612=Notch=WD(100=19.9),PF0006612=Notch=PU(15.0=3.1)
A:
NA
C2:
PF0006612=Notch=PD(82.5=22.9),PF068168=NOD=WD(100=39.6),PF076847=NODP=PU(4.8=2.1)
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:
TCCCACCCAAAATCGAGGAGA
R:
CCGTCCCACTCACACTCAAAG
Band lengths:
352-1110
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]