GgaINT0124456 @ galGal4
Intron Retention
Gene
ENSGALG00000002375 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:HGNC:7881]
Coordinates
chr17:7837831-7838483:+
Coord C1 exon
chr17:7837831-7838047
Coord A exon
chr17:7838048-7838392
Coord C2 exon
chr17:7838393-7838483
Length
345 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGT
5' ss Score
7.97
3' ss Seq
GCATGGTTTTGTTCTCAAAGACC
3' ss Score
3.89
Exon sequences
Seq C1 exon
GTGAAACGGCGGAGCCCGCGAGGAACTCCCAGCTGTATCCTATGTATGTGGTGGTGGCTGCACTGGTCTTGCTTGCCTTCATTGGAGTGGGAGTGCTGGTGTCCCGCAAGCGGCGCAGGGAGCATGGCCAGCTCTGGTTCCCAGAGGGCTTCAAAGTGACGGAGTCGAGCAAGAAGAAGCGCCGGGAACCACTTGGGGAAGATTCTGTTGGACTGAA
Seq A exon
GTGAGTAATGGGGTTGTTATCTGATAGGCACGGCAGAGCGGGGCTGTCTGGGGGCTCTTCTGAACCGTCCCTTCGGTTTTGTTCTCTAAGGCATCATAGAGGAGCGGTGGGGAGGAGAGAAGTGGGGGTTTGTATTGTTCTGCATTGGGAAAACCACACTTTAGTTTGGAGGAGGTTTTTTGATGCTTCTTGGTCCGTTGGTTCTTGGGAGAGTACGAAAGGCACCTTGAGGGGAATGTCCCGAAAATCAGCCTCGTTGATTCTTCAGTGCATGCATAAAGCACAGCCCATCACATATCAGTCCCTGCAGAGGAACTAATTCTTGGCATGGTTTTGTTCTCAAAG
Seq C2 exon
ACCCCTCAAAAATGCTTCTGACGGCACGCTGATGGACGACAACCAAAATGAGTGGGGTGACGAGGAGACCCTGGACACCAAGAAGTTCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002375:ENSGALT00000003754:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.233 A=NA C2=0.903
Domain overlap (PFAM):
C1:
PF076847=NODP=PD(14.3=12.3)
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:
AGGAACTCCCAGCTGTATCCT
R:
TGAACTTCTTGGTGTCCAGGG
Band lengths:
286-631
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]