HsaINT0146726 @ hg19
Intron Retention
Gene
ENSG00000120341 | SEC16B
Description
Protein transport protein Sec16B [Source:UniProtKB/Swiss-Prot;Acc:Q96JE7]
Coordinates
chr1:177901833-177902447:-
Coord C1 exon
chr1:177902349-177902447
Coord A exon
chr1:177901942-177902348
Coord C2 exon
chr1:177901833-177901941
Length
407 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGC
5' ss Score
8.99
3' ss Seq
TTTCTTTCTCCACAAAGCAGGAG
3' ss Score
3.66
Exon sequences
Seq C1 exon
AGCTCAGGGTTTGGCTGGTTCAGCTGGTTTCGATCGAAGCCCACCAAGAACGCATCCCCCGCTGGAGACGAGGACTCCTCAGACAGCCCTGACTCTGAG
Seq A exon
GTAGGCTCTGTGGGAGGGGGAGGATGCCCCTCTCTGTGGGTCTTTCAGAGGGAGCTGCCTCAGCACCTAGGAGCTCTCAGAGCTGGCACCTGAGTCTACCCCAGGCCACATGAGACAGAGGTTTTGTGATGGGATATGGTGGGAAATGAATGGGTCCTGTGAGGGCAAAGGCAGATTAAAAAAGCTTTAAAAAGTTTGGATGAAGAAATGTAACTTTAGAGGGTCAGCAGTAGGGAGCTAGTGTGGATTGTTGAGCAGAAGAGTGGGATGAGGAGGGGGGTTTTGGGGAGTGCCCAGCAGCAGTTTGTGGCAAGGCCGCCATCGTGAGTGTGGGAACACAAATTGGCGGGCATCAATTTGTTAACTGCCAATGTTGCCAATGCTGCCTTTCTTTCTCCACAAAGCAG
Seq C2 exon
GAGACCCCCAGAGCATCTTCTCCCCACCAGGCTGGCCTGGGCCTCTCACTGACACCTTCCCCTGAGTCCCCACCTCTGCCGGATGTTAGTGCCTTCTCCAGGGGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000120341-SEC16B:NM_033127:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.879 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCAGGGTTTGGCTGGTTCAG
R:
CTCTGCCCCTGGAGAAGGC
Band lengths:
206-613
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)