HsaINT1025117 @ hg38
Intron Retention
Gene
ENSG00000204301 | NOTCH4
Description
notch 4 [Source:HGNC Symbol;Acc:HGNC:7884]
Coordinates
chr6:32215226-32217067:-
Coord C1 exon
chr6:32216945-32217067
Coord A exon
chr6:32215386-32216944
Coord C2 exon
chr6:32215226-32215385
Length
1559 bp
Sequences
Splice sites
5' ss Seq
CAGGTTCAC
5' ss Score
1.23
3' ss Seq
GACCCATCTTCCCACCCCAGGCC
3' ss Score
8.48
Exon sequences
Seq C1 exon
GCTTTGAAGGGCCACGCTGTCAAACAGAGGTGGATGAGTGCCTGAGTGACCCATGTCCCGTTGGAGCCAGCTGCCTTGATCTTCCAGGAGCCTTCTTTTGCCTCTGCCCCTCTGGTTTCACAG
Seq A exon
GTTCACAGGGGAGGCACTGGAAAGAACTGGCAGAATATTTTATTCCATTTGGGTTGGGGCAGAGTTCATTGGTGGGTGTTTGATGGTTGGGATGTGAGAATAGAATGAGAATGGTATCCTTTAAAGTTATTTAGTGTAAAACCTGCACAATTGTACAACCATGGGGACAAGGGCAGGGGTTACCGTAGGGCCCACATGGGCCCAGTGTAAATGGTGTGATTGCGGCTTGGGAGCAGAGGACGGGGCTCAAAGAAAAGGCATTCACTTGCTTATTTAGCAAGCACTTACCAACTGCCTACTATGCCAGATACGGAGGCAAATCTGAGTAAGACAGTTGCCATCTTCATGTGACTTTAAGTCTAATACAGAGAGACCAACAAGTCTCCTGTTGATCATAGCCCACAGAGGTGCTCTGAGAGAAAAACGTGCAGGATATTACAAGAGCACAGAGGACCAGCCAACCCAGACTAAAAATGGAGGAGGTGATGGCTGAGATGAGTCTTGAAAGATAAGCAGAGGCTGGGCGTGGTGGCTCACGCCTATAGTCCCAGCACTTCGGGAAGCCGAGGCGGGTGGATCACCCGAGATTAGGAGTTCGAGATCAGCCTGGCCAACATGGTGAAACCTCGTCTCTATTAAAAATACAAAAATTACACTTTGGGAGGCCGAGGCGGGTGGATCATGAGGTCAGGAGATCGACACTATCCTGGCTAACACGGTGAAACCCCATCTCAACTAAAAATACAAAAAAATAACTGGGCGTGGTGGCGGGCGCCTATAGTCCCAGCTACTCCAGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGTGGCAGAGTAAGACTCCACCTCAAAAAAAAAAAAAAATACAAAAATTAGCCAGGCGTGGTGGCGGGCGCCTGCAATCCCAGCTATTGGGGAGGCTGAGGCAAGAGAATCGCTTGAACCTGGGAAGCAGTGGTTGCAGTGAGCTGAGATCACTCCACTGCACTCCAGCCTGGGTGACAGAGCAAGATTCCATCTCAAAAAAAAAAGAAGGAAGGAAGGAAGGAAAGAAGGAAGGAAGGAGAGAAGGGAAGGAAAGGAAGGAAAGGAGGAAATGAGGAAAGAGAGAAAGATAGAAAGATGGATGGTCAGGAGTCTGTCTAAATAGAGTGCCAGATAGTGTGTTTTAGCTGGAGATAACTGCATGTGCAAAGACACAGATGGAAGAAAAGCCCACCCCATTTAAGGAACTGTAAGAAAGTCAGAGTTAAGGGTACAGCAAGGCAAAGATGAGAAACACAGCTGTTGTACAAATGTCATGTCCTGCAGGACTCTGCATATCATTCTGAGAAAGTTAAACAATATCTTAAAGGCAATAGGGACCCATTGAAGGACAGGTTCATGGGTTCATAGGGAGTGAGTAAGGCAAGCATAAGAAGTGGCTTTGGCCCAATGAAGGATGTGGCTTTGGCCCAATGAAGGATGTGGAGGAGCTGTTTTCTTTTTGACCCATCTTCCCACCCCAG
Seq C2 exon
GCCAGCTCTGTGAGGTTCCCCTGTGTGCTCCCAACCTGTGCCAGCCCAAGCAGATATGTAAGGACCAGAAAGACAAGGCCAACTGCCTCTGTCCTGATGGAAGCCCTGGCTGTGCCCCACCTGAGGACAACTGCACCTGCCACCACGGGCACTGCCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204301:ENST00000375023:11
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:
PF0764510=EGF_CA=PD(25.0=23.8),PF0000822=EGF=PU(90.3=66.7)
A:
NA
C2:
PF0000822=EGF=PD(6.5=3.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTTGAAGGGCCACGCT
R:
CGTGGTGGCAGGTGCAGT
Band lengths:
270-1829
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains