GgaINT0124461 @ galGal4
Intron Retention
Gene
ENSGALG00000002375 | NOTCH1
Description
notch 1 [Source:HGNC Symbol;Acc:HGNC:7881]
Coordinates
chr17:7840414-7842342:+
Coord C1 exon
chr17:7840414-7840511
Coord A exon
chr17:7840512-7840747
Coord C2 exon
chr17:7840748-7842342
Length
236 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGG
5' ss Score
8.76
3' ss Seq
AACTTCATCTGGGTTCCTAGGAG
3' ss Score
5.54
Exon sequences
Seq C1 exon
GCAAGTCAGCACTGCACTGGGCAGCTGCTGTGAACAATGTCGAAGCCGCTGTCGTCCTCCTGAAGAACGGTGCCAATAAGGATATGCAGAACAATAAG
Seq A exon
GTAGGGTCTTCGGGGCTGACCAGTGGGCAGAGAAAGAAGTATTTGGGCACTGTGTTAAAAGGCACTTTGAGCCTGTAATACAACACTGTCTGGCACTGAGGCTGTTGTTCTGCTGTGACTCCGGGTGTGGGGTTTGGTGTTAAGGGTTATGCCGTATGCAGTGCTTGGTAGGGGGTACAGAGTGGTGCTACCTGGAGGACGAATGAGCACAGACCTAACTTCATCTGGGTTCCTAG
Seq C2 exon
GAGGAGACCCCGCTGTTCCTCGCCGCCAGAGAAGGGAGCTACGAAACAGCCAAGGTTCTGCTGGACCACTTTGCGAACCGCGACATCACGGACCACATGGACCGGCTGCCGCGGGACATCGCGCAGGAGCGCATGCACCACGACATCGTGCGGCTGCTGGATGAGTACAACCTGGTGCGGAGCCCTCCGCTGCACAGCGGCCCTCTCGGGGCCCCCACGCTGTCCCCCCCGCTCTGCTCCCCCAGCAGTTACATCGGCAACCTGAAGCCGGCCGTGCAGGGCAAGAAGGCCAGGAAGCCGAGCACCAAGGGCCTGAGCTGCAACGGCAAGGATTCCAAAGACCTGAAAGCCCGGAGGAAAAAATCACAAGATGGAAAAGGCTGTCTGCTCGACAACTCCAGCGTGCTGTCCCCAGTGGACTCCCTGGAGTCACCCCACGGGTACCTGTCCGACGTCGCCTCCCCTCCGCTGATGACTTCTCCGTTCCAGCAGTCCCCTTCCATGCCTCTGAACCACCTGCCTGGCATGCCCGACGCCCACATGAGCATCAACCACCTCAACATGGCAGGGAAGCAGGAGATGGCCCTGGGCGGCTCTGGCAGGATGGCCTTCGAGGCGGTGCCGCCGCGCCTCTCGCACCTCCCCGTCTCCAGCCCCAGCACGGCGATGAGCAACGCCCCGATGAATTTCTCCGTCGGCGGAGCTGCCGGCCTGAGCGGGCAGTGCGACTGGCTGAGCCGGCTGCAGAGCGGCATGGTGCAGAACCAGTACGGCGCCATGCGGGGCGGCATGCAGCCGGGCACGCACCAGCAAGCACAGAACCTGCAGCACGGCATGATGAGCTCCCTGCACAACGGGCTGCCCAGCACCAGCCTGTCGCAGATGATGAGCTACCAGGCCATGCCCAGCACCCGGCTGGCCTCCCAGCCCCACCTGCTGCAGAACCAGCAGATGCAGCAGATGCAGCAGCCCGGAATGCAGCCGCAGCCCGGAATGCAGCCGCAGCCCGGCATGCAGCAGCCTCAACAGCAGCCCCAGCAACAGCCCCAGCCGCAGCAGCACCACAACCCCGGCTCCAACGCCAGCGGCCACATGGGCCAAAATTTCCTCGGTACTGAGCTGAGCCAGCCCGACATGCAGCCGGTGAGCAGCAGCGCCATGGCGGTGCACACCATCCTGCCCCAAGATTCGCAGCTGCTACCCACCTCTCTGCCGTCCTCCCTCGCGCAGCCCATGACCACCACGCAGTTCCTGACCCCCCCTTCCCAGCACAGCTATTCCTCCCCGTTGGACAACACCCCCAGCCACCAGCTCCAGGTGCCCGACCACCCCTTCCTCACTCCCTCTCCGGAGTCTCCAGACCAGTGGTCGAGCTCCTCGCCCCACTCCAACGTGTCCGACTGGTCCGAGGGCATCTCCAGCCCCCCCACCAGCATGCAGTCGCAGATGGGACACATCCCCGAGGCCTTCAAGTGAGACCCAGTGGGGCTCAGGGACTGCAGCCTGAGAGACAGCTGCTTTTTTGTTGTTCAACAGGACGCTGGATGCTTTTATTAAAGGATCCTTTTTTTTAAAATACGTTTTTATACAAAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002375:ENSGALT00000003754:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.212 A=NA C2=0.833
Domain overlap (PFAM):
C1:
PF127962=Ank_2=FE(34.4=100)
A:
NA
C2:
PF127962=Ank_2=PD(32.3=6.1),PF119363=DUF3454=WD(100=13.0)
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:
CTCCTGAAGAACGGTGCCAAT
R:
AGGTTGCCGATGTAACTGCTG
Band lengths:
305-541
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]