HsaINT0146735 @ hg19
Intron Retention
Gene
ENSG00000120341 | SEC16B
Description
Protein transport protein Sec16B [Source:UniProtKB/Swiss-Prot;Acc:Q96JE7]
Coordinates
chr1:177927975-177929538:-
Coord C1 exon
chr1:177929477-177929538
Coord A exon
chr1:177928111-177929476
Coord C2 exon
chr1:177927975-177928110
Length
1366 bp
Sequences
Splice sites
5' ss Seq
TAGGTATAG
5' ss Score
5.16
3' ss Seq
CCTAAATTTTTTCCATGTAGGGA
3' ss Score
7.46
Exon sequences
Seq C1 exon
GTTATTCTTAATGATTCCGAAGAGCAAGAGGAGATGAGAAGTTTCTCAGGACCCTTGATTAG
Seq A exon
GTATAGTGCTGTAAGAGCTGCTGAGTAAGGGCTTTTGAAACCTAGAAAATCTTCCTGCCCAGATCAGCATTTTGGAGATTTGTTCTTGGTTTCCTTGGAAAAAAATATCTGTCCTTGTTGGAGTGGAATTCTCTGTGCTGCAAGATAGAACCAGATGTGGCCTGAGTCATTTTGACAAGCCATTCAATAGTTGAAGGACAGAAAGAAAAATTAGCATGACAGTTTAGAAATCTAAAACCAGTTCCATTATGCAGAGGCTGCATGGTTGGAAGTTTTAGCATTCCGTGTGCTTGATAGATGTTAGTAGAAAAGTGGAGCATCGCCTGGGAAGTCACTGACAAGTGGATCATAGCAGAAACAATTCTTGTAACAGTGGCTTTTTCCTGGAGAGGTAAATAAGATCGGCAGTGTTCAAGTTACAGAACAGTGTGCAAGTGAGCCCTCTGCAGTACTGAACTAGGACTGCTTTTAAATGTCTAGTTATATTTCTGATAAATGTAACTCAGGGCATCTTTGTTGAGGAGAGAGTCCTTGCTGGATGACAGCCCACGTGGGTCTCAGGCTCAGGCGTCTTACTGACTAGGAATACCATGGTGGACAGGTCAGTTAGCCCTCTCTGAACCTTAGTTTTCCCCTTGAGAAATGGTATAACACCTGCTCTCCCTACCCGAGGCTTGTCTATGAGTCTCAAGTCAGATTATGCACATGGAAAGTATCATCACTACTATATAAATGTATTCCTCAAATGGCATTTGACGGTTCCCTCAAGTAAAAATGAGTGTTATCTCTTTCTTACAAACAGGTATACAGATATGGGGCAAAAAAGCGAGTTGGGTATTCAAACACTGGGGTACTAAGCCTAACTTGGCTTTGATGTTATTGGATAATCTTGAGCAAATCATAATGCCAATCATATTGATCACTTAATATATGCCACACAATTTTCTAATTCCTTTTTGTATGGAGGTAGGTCCTTTTACTGTCCCTATTTTAGGGGACAAAGCTGAGGCTCAGAGGAGGTAAGAAACTTGTCTAAACAGAGAAGTGGCAGAGCCAGATTTAGATCCAGGGTTGTCTGACTCCAAAGTCTGCTTTTACTTGCTTTCCTGTGCAGTGACTTCAGGTCTCTGAGCCTCTGTTTCTTCATCTATAAAGGGGGTGCATGAGAGAATCTCTGAAATTTCTTCTTGTTCTATAAGAAAATAACTATCCTATAGCTATAGACTCATTACCTTAGCCCTGGCTTGTCAGATTTCTATCTCAATCACAGCCCAGCCAGCACTTGCACACTTAGGAGGAGCCTGGGGTCCGAAACAGGGAAGTGTCTGCCTGCTCACTCTTTGCTCCCTAAATTTTTTCCATGTAG
Seq C2 exon
GGAAGATGTACATAAGGTGGATATTATGACGTTTTGCCAGCAGAAAGCAGCTCAGAGCTGCAAATCTGAGACACTGGGGAGCAGAGACTCAGCTCTACTGTGGCAGCTCTTGGTTCTCCTTTGTCGCCAGAATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000120341-SEC16B:NM_033127:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.512 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF129322=Sec16=FE(19.6=100)
A:
NA
C2:
PF129322=Sec16=FE(44.1=100)
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:
GTTATTCTTAATGATTCCGAAGAGCA
R:
CCCATTCTGGCGACAAAGGAG
Band lengths:
198-1564
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)