HsaINT0146178 @ hg38
Intron Retention
Gene
ENSG00000159307 | SCUBE1
Description
signal peptide, CUB domain and EGF like domain containing 1 [Source:HGNC Symbol;Acc:HGNC:13441]
Coordinates
chr22:43210922-43212592:-
Coord C1 exon
chr22:43212425-43212592
Coord A exon
chr22:43211084-43212424
Coord C2 exon
chr22:43210922-43211083
Length
1341 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TGCCTTGTGTCCCCCGGCAGTGC
3' ss Score
8.77
Exon sequences
Seq C1 exon
GCCAGTGTTCTCCAGGCTTCTTCTCGGCCGATGGCTTCAAGCCCTGCCAGGCCTGCCCCGTGGGCACGTACCAGCCTGAGCCCGGGCGCACCGGCTGCTTCCCCTGTGGAGGGGGTTTGCTCACCAAACACGAAGGCACCACCTCCTTCCAGGACTGCGAGGCTAAAG
Seq A exon
GTGAGCATGCCCTCCCCACCACGCCCGCCCACCCCGAGAGGCAGGGCTGCACTGCTCCGAGAGGCTTCCCCGAACCCCTCTCATCTCCTCCATGTGGCGAACCTCCCAGCTCAGAGGAGGAGCCTGGAGCTGTCAGGCGTGGGCGTGGGTGACCCACTGTGCCCCGCATTAGGACAGGGACACCTTATAGCTGAGAGCTTTCTGAGCTCCAGGGGGAACAGCAGCTCCTCGGAGCACTGGGGAGGGCTCTGGGGACAGGAGGCCTTGAGCAGCATCTAGAAGGGAGGTTGGGAGGGTGAGGAGGGGGCAGGAGTGTGGGGGCAGGAGTGTGGGGGCAGGAGCGGGATCAGGGCATCACCTCAACTGCTGTCTGTTCAGGGCATCTGGTCCCACCCAGGTCTACATCCCGTCTTCCCTCACTCACCAACTCCCCCAAATCCTCCCCATTCTCAGCTGCTGACCCTGCTTCCCCACCGTGCTCCCTCTCAGTGTCTGTCTGTCTGTCCAGGTGGCCTGGCTCTCAGCCCCCTGGAGCCAGCCACATCACCAGATACTCCCCTGCACATACAAACTGTTCTGAATTTGCCCATTTAAAAAAAGAAGCCAGGTGCGGTGGCACACACCTATAATCCCAGCACTTTGGGAGGCCAAAGGGGGTGGATCACCTGAGGTCAGAAGTTTGAGGCCAGCCCGGCTAGCATGGCAAAACCCTGTCTCTACTTAAAAAAAATACAAAAATAATTAGCCGGGTGTGGTGATGTGCACCTGTAATCCCAGCTACTCGGGAGACTGGGAGGGGAGGATCGCTTGAACCCAGGAGGTGGAGGTTGCAGTGAGCCGAGATGGCACCATTGCACTCCAGCCTGGGTGACGGAGCGAGCTCCATCTCAAAAAAAAAAAAAAAGAATTGCCCATCTCTAGCCCCCCGCCCCGGCACCCCTCAGACTCCGGCCGCCTGTCTCTCCTGCCCCAGCAACCTTGTAGAAAGAGGGTTTGGCCTAGCTGGCTCCACTTCCCCTCCTCCCTGTCTCCCCCGCACGCCTCCGGCCACATCATCGCCCCCGCTCTCCCTGAAAATGGCTCCCATCAAGGTGGCCTGTGTGGTCCCTGTTTTGCTGGAGCCAACATCACATCAATCTGCCATGTGACCCCCACGCCAAGGGCTCTTCCTGGCCATGGCGGAGTGAGGGTGGTGGGAGGTCATGGGGCGGTGGGGAGGAGCCTTGAACTCTGTGCCAAAACAGACCTCGAGGGCATGAGAGGTCCTGGGGACAGCACCCCAGTGCTGCCCTTTCCCTGCACCCCTCCACACCCACCACACTGCCTTGTGTCCCCCGGCAG
Seq C2 exon
TGCACTGCTCCCCCGGCCACCACTACAACACCACCACCCACCGCTGCATCCGCTGCCCCGTCGGCACCTACCAGCCCGAGTTTGGCCAGAACCACTGCATCACCTGTCCGGGCAACACCAGCACAGACTTCGATGGCTCCACCAACGTCACACACTGCAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000159307:ENST00000360835:17
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:
PF076998=GCC2_GCC3=WD(100=84.2)
A:
NA
C2:
PF076998=GCC2_GCC3=WD(100=87.3)
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:
GCCAGTGTTCTCCAGGCTTC
R:
TTTGCAGTGTGTGACGTTGGT
Band lengths:
329-1670
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development