GgaINT0038683 @ galGal3
Intron Retention
Gene
ENSGALG00000002922 | NOTCH2
Description
NA
Coordinates
chr8:4204759-4206585:+
Coord C1 exon
chr8:4204759-4205018
Coord A exon
chr8:4205019-4206249
Coord C2 exon
chr8:4206250-4206585
Length
1231 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
CTTACGTCTTCATCCTACAGGAA
3' ss Score
10.7
Exon sequences
Seq C1 exon
GTGTCGAGAAGGCTATCTTGGAGACTACTGCCAGTACAGGAACCCCTGTGAAAGCAATACGTGTAAGAATGGGGGAACCTGTGAAACCACGTCTCTGATAGGAAAGGCCACCTGCAAATGTGCTCCAGGGTTCACAGGAGAGGACTGTCAATACTCTGAATCACACATCTGCTATGTGTCCCAGCCCTGCCTGAATGGAGGGACGTGTCATCCTCACAGCCAGGAAACATATGAGTGTGTCTGTCCTCCAGGTTACACAG
Seq A exon
GTGGGATTCTGCATTTGTGCCTTCAGACCCCTTCAGTTGTGAATTCCCCTGTCCTAGAACGTTTGGGGGCAGTTGCAGCTTGCTCTCAAATTTAATGGCTCCAGCACAGGAAATGAGATGAAGTCCAAATGACTTCATGATAAAAATAAGAAATAAAAAATAAAAGAGCTAAAGGGGGTGGGGAGGGAAGGTCAAACTCCATACCCTTTACACATAAACAGAAAGATATTTATGTCTTGTGGGGCTGTCCCCGTGGGAAAACTGACTGTAGAAGCTATCCTGAAATGGCTGTTAGAATTTTAATTCACAATCTACCTTCTAGAGAAAATGAAGTCAATTTGGCCAGCAAAATCTTTCAGTGGGAAAATGTTAATTGGTTGCCTGAGGAGAAGCATGGAAATTCCCACCTCCCTTTCTTGAAGGGAAAGTAGAACAAGAGAGTGACTGGCAGTGTGGTACGATTTCAGGTCGGTGGGTAATTTTTATAAATCACAACGTTCTGTATCTTGCTGGTAATGCATANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAAGTCAATTTGGCCAGCAAAATCTGTGAGTGGGAAAATGTTAATTGACCCGCTAAGAGGAAAAGCAAGGAAAGCCGCACGTCGCTTTCTTGCCGGCAAAGGCGAACAGATAACGGATTGGTGCTCTGTGATTATTACAGGCCATTCAGGAAATTTATAAATCACAACGTTCTGTATCTTGCTGGTAATGCATAAATAGGTTACAGGCTTTCTCCCGTAACCAGCAAGTTAATTTTGTTTCAGGTATTGTAACATATAAGCTAATTCCTATAATCATTTTGCACACGTGCTTTAGGTTAAGATGTAGTACAGCAGCCATTCTGGGGTAGCCTGAAGCGTGACGTGTGGAGCTGTTTTCCATATTCATTTCTTACGTCTTCATCCTACAG
Seq C2 exon
GAAAGGACTGCCAGTGGATTGATGCCTGTACCTCTCAACCTTGTGCCAATGGAAGTACATGTACCGTGTCTGGACATAAGTTCTCCTGCATCTGTCAGTCTGGCTACACTGGCCAGAAGTGTGAGATAGATGTGAACGAATGTGCCACGTCAGGCCTTTGTCACCATGGTGGGACCTGCATCAATTTGCCTGGTTCGTTCCGATGCCAGTGTAAGCCAGGCTATACAGGGCATCGCTGCGAGAGCAATTATGTGCCGTGTTCTCCATCACCTTGCATGAATGGAGGAACTTGTCATCAAACAAGTGACTTCACCTTTGAGTGCAACTGTCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002922:ENSGALT00000039988:3
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:
PF079748=EGF_2=PD(28.6=11.4),PF0000822=EGF=WD(100=37.5),PF0000822=EGF=PU(90.9=34.1)
A:
NA
C2:
PF0000822=EGF=PD(6.1=1.8),PF0000822=EGF=WD(100=27.4),PF0764510=EGF_CA=WD(100=38.9),PF0000822=EGF=PU(81.2=23.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGGAGGGACGTGTCATCCT
R:
TGCAAGGTGATGGAGAACACG
Band lengths:
343-1574
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]