HsaINT0146731 @ hg19
Intron Retention
Gene
ENSG00000120341 | SEC16B
Description
Protein transport protein Sec16B [Source:UniProtKB/Swiss-Prot;Acc:Q96JE7]
Coordinates
chr1:177933306-177934302:-
Coord C1 exon
chr1:177934182-177934302
Coord A exon
chr1:177933415-177934181
Coord C2 exon
chr1:177933306-177933414
Length
767 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
CTCCTGTCATTTTGCTGCAGATC
3' ss Score
9.8
Exon sequences
Seq C1 exon
TGCCAAGGCAACGGAGTCCTTATATCTGGCACGAAGATTACCGAGAGCAAAAGTACCTTGATGAACATCATTATGAAAACCAGCACAGTCCATTTGGAACAAATAGTGAGACCCACTTCCA
Seq A exon
GTAAGTGTGAAAGGAGAGGCCAGTTTGACATGATGTTGTCAAACTCAGACTATGTCGGGCAAATCTTCTGGCGTCTGATGCTGCCATCTCACCTCCAGAAGCCCATGTACCTTTGTTGTAGCCACAGGGATATGGGAATATCCCAGGATGGGCCTGGCCAGCTGTTAATATGGACCCTGGGAAGGGAGGTTCTTATCACTGACAGTCTGTTCCCAAAGCTGGGCGAGTCTGAGTCCTGTGAGGTTCCTTGAGGTCTGTCCTAAAAGAGGACTTTAATTCTGTGTTGGCCTTAGAACAGATATGGCCTAGCAAAAGTTCTCACGATTAGGTCATGAGAACTTACCTGGTGCTGTGGTGCTTTTCCTCAGCCTACGCCTGAGCCCTGAGAATGGGCCATCTCCCTGTGGTAAGACAAGACAGGGAAGAGAGTTTTGCTCAAGCATCTGTCCTGGTGCTTGCAGCTGTGGAATTCACCAACCTAAACACTCTGATGTAAGTCATTCCAGAATGTCAGGCTGTAGAGACCAACCCTTCTCATCAGGGCCTGAGGCCACTTCCAGCCACTGAGCTGTGGAACTCCAGCACTCCTGTTTTTCTGGGATTAGTAGATTGAGGTGGTGAGTAGGAGGAAAATGCTTTCTCCTATGGCACCCAGGCTGACATGGTACCTGCCCACGCTTTGGAGCAGGTCAGCTTCCGGCGGAGAGTGCCTCAGCCTTGCTGGCTTGCCCAGGACCCCGCTCACTGCTCCTGTCATTTTGCTGCAG
Seq C2 exon
ATCTAACAGTAGGAACCCTTGTAAAGACAGCCCTGCTTCCAACTCTGGACAGGAGTGGCCGGGGGAGCTGTTTCCAGGGAGCCTGCTTGCTGAGGCCCAGAAAAATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000120341-SEC16B:NM_033127:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.713 A=NA C2=0.865
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAAGGCAACGGAGTCCTTAT
R:
TTTTTCTGGGCCTCAGCAAGC
Band lengths:
224-991
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)