HsaINT0146719 @ hg19
Intron Retention
Gene
ENSG00000120341 | SEC16B
Description
Protein transport protein Sec16B [Source:UniProtKB/Swiss-Prot;Acc:Q96JE7]
Coordinates
chr1:177909745-177911175:-
Coord C1 exon
chr1:177911035-177911175
Coord A exon
chr1:177909850-177911034
Coord C2 exon
chr1:177909745-177909849
Length
1185 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
CATCTGGAAACCTGGCACAGCTA
3' ss Score
-0.93
Exon sequences
Seq C1 exon
GTGTATAAGCTCCTTTATGCTTCCCGTCTGGCAGATTATGGCCTCGTGTCCCAGGCTTTGCATTACTGCGAAGCCATTGGTGCAGCTGTCTTGAGCCAGGGAGAGAGCAGTCACCCTGTGCTATTAGTGGAACTCATCAAG
Seq A exon
GTGAGCCTCTCAAAGGGTTCTGTGCAGTTGTTTTATCTTCACTATTCAGAGAAAGCCATCGTAGAGCAGCTTAGACTCTACATTTCATCTTCTTTGAACATGCCATAAAATTGGAGCCCACGGCCATCTTTGACCATGTATGCATGCCCAGATGCGATAAGCAGAGGCCCAACACTACACAAAGAAGGATCTTCTCTGGGCGGGTGGTGGTGGGATTGGAGACTGGAAACCATGTGTGTGTTACTCAAGAAATTCATTCTTGCATCTGCTTTTCTGGTACAGTAAAACTACATGCTACGGTGAACCATTCTAATTATAAAAGCTGGGCTTAGAAAATATATTTTAGTGATTAAAAGAGTAAATGATCCTTATTAAAATGCTTTTAAATGCATGGAATATTTTGTCACATGTGAGGTACATTTAAAATAGAAAACAAAAACATATCAACCTTTAGTTCCTAGGAAAGAAAACAACAATCAAGCAAATAGTTGTTTCAATTAATTGAAGAAAAATCCATTAGCTAGAGAGTAAAAAAGCAGCCTACCCTTAAATTTTTGCTTTGCCATAGATGAGGCCCAAGTGCTGGCTTCTTTAACGTATAAAATTTGTGGTGGTGAGCCTCCCCATACCCTGAAGTTTCTGCCAACAGGTTGATGGTTGCAAGGAGCTCAGGGATCCAGAATGAATTATTAGAAAAGTTTCAGTAACTAAAACTTGTTTATGGAATAAATCCTTGAAATACAAAGTAACATTAGCATCACCTGGGAGCTGGTTAAAAGTGCAGACTCTTAGGCCCTGCCCAGACGTATGGAATCAGAATTAGCATTTTAACAAGTTTACAATTAGAATTTTAACAAAATTCCTATGTATACCCTAAGTTTGAGAAACACTGTTACAGAGCAGACAGCTTTGCAGAGAAATGAAGCTGAGTAACTGTTTCTCCTCATATTTTATTTAGAATCTAGCACCCAAGACGGGTTGTTTATTTATGTTGCAATTTTGGGAGGATATCTGCTGAATTTGCTGTTTTTCGATTATTTTTTATAATGTAATTTACAAGTTAGTTAAGGCTCTCTTTCTCCTTTTTCCTTGTTTTCTCTTCCCCGTTGTCTTTCCATTTCTCTTCCCTCTCTCTCCTCTCCTCTCTTACTTTCTGCCCCTAACCCATCTGGAAACCTGGCACAG
Seq C2 exon
CTAGCAGAGAAACTGAAGCTGTCAGATCCTCTGGTTTTAGAAAGACGCAGTGGAGACAGGGACCTGGAGCCAGATTGGCTAGCGCAACTTCGGAGGCAGCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000120341-SEC16B:NM_033127:16
Average complexity
IR-S
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:
PF129312=Sec16_C=FE(16.8=100)
A:
NA
C2:
PF129312=Sec16_C=FE(12.5=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:
GTGTATAAGCTCCTTTATGCTTCCC
R:
CTCCAGCTGCCTCCGAAGTT
Band lengths:
246-1431
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)