HsaINT0146733 @ hg19
Intron Retention
Gene
ENSG00000120341 | SEC16B
Description
Protein transport protein Sec16B [Source:UniProtKB/Swiss-Prot;Acc:Q96JE7]
Coordinates
chr1:177929926-177930869:-
Coord C1 exon
chr1:177930725-177930869
Coord A exon
chr1:177930075-177930724
Coord C2 exon
chr1:177929926-177930074
Length
650 bp
Sequences
Splice sites
5' ss Seq
CTGGTGGGT
5' ss Score
6.29
3' ss Seq
CTGTGTCTGTTGGTCAGAAGATG
3' ss Score
1.39
Exon sequences
Seq C1 exon
CCATCATTGGCTAGTGAGTCCAACCTTCTCCAGCAGCGTGAGTCTGGTCTCAGCTCCAGCAGCTATGAGCTCAGTCAGTACATCAGAGATGCCCCGGAGCGGGATGATCCCCCAGCTTCAGCAGCTTGGAGTCCAGTTCAGGCTG
Seq A exon
GTGGGTTCTAAAATGATCAGAAGAGTTGATTGAATCTGATGTGGAAGGGCTGGGTGGCAAGTCTCTGGGAAAGTCAGCCTTACGATGGATCATTGTCCACCTCATTTGCTTATGTAGGTCACCTGGGCAGAGAGGTCAACTTTGGTTCCATTTTCTCTCTTTTTGCTTGTAATAGTAATTGCATCATAGCTGATTCCTGGAAGGGAACACTGCCCCTATCCATTATCAAGTTGGGAAAGGAGGCACTCAGTGGTGCTTTTAAGAAAGGGAAGACCAGAGAGAATTAGGAAAAGCAAAAGCAAGATGCAAAGCTTCATTGCTTTGTCTGGATGTAGGAACTTTGTCATGAGTATAGAGGCCATGAAAGCCAGAGACTCCTTGGCCTCTCAGCATCACTGAGAGTCTGGGCTGAGAGCATTATCATTTGGACTGAATCATCAAGCCCACGCATTGTATTCTGACACCTTCTCAGAGGCTTAAATCTGACTGGAGCAGGGAACATGGGCTTCTTCTAATTACACAACCCACCCAGAATCTTATTTTGGTTCAGGCAGAATTTGGGCAGAAATACATCTGTGGCATATTCCTAAACTAAAGAAAAGTGATGGAAGTAACGCTAACAATGTCCATCTGTGTCTGTTGGTCAGAAG
Seq C2 exon
ATGTCTCCTCAGCTGGTCCCAAAGCACCCATGAAGTTCTACATCCCTCATGTTCCTGTGAGTTTCGGGCCAGGAGGTCAGCTGGTGCATGTAGGTCCCAGCTCTCCCACTGACGGGCAAGCAGCCCTTGTTGAACTGCACAGCATGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000120341-SEC16B:NM_033127:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.883 A=NA C2=0.386
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF129322=Sec16=PU(33.3=68.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCATCATTGGCTAGTGAGTCCA
R:
CTCCATGCTGTGCAGTTCAAC
Band lengths:
294-944
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)