HsaINT0146690 @ hg19
Intron Retention
Gene
ENSG00000148396 | SEC16A
Description
SEC16 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:29006]
Coordinates
chr9:139350505-139352036:-
Coord C1 exon
chr9:139351896-139352036
Coord A exon
chr9:139350619-139351895
Coord C2 exon
chr9:139350505-139350618
Length
1277 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCTG
5' ss Score
4.87
3' ss Seq
TGATTTTTGCCCGTGTCTAGATG
3' ss Score
8.44
Exon sequences
Seq C1 exon
GTGTTTAAGTTCATCTACTCCTGCCGCCTGGCGGAAATGGGGCTGGCCACGCAAGCCTTCCACTACTGTGAGGCCATCGCGAAGAGCATCCTGACGCAGCCGCACCTGTATTCCCCGGTGTTGATCAGCCAGCTTGTGCAG
Seq A exon
GTGCTGCCCCTGGCGCCTGTCCTCGGGATGCTGTGCTGACTGCAGGGAAGGAGGGCTTGCCAGAGCCCCCGGGCATGGGGGTAGCGATGGTTCAGACGCGCATTGTGGTAGGCGCTCAGAACCTGCCTCTTGGGCGGATAAAGATCTTTGAATGGCTTCGTGTTTTGCGTCTTAGCCTGGGAACTCTCAGGCACCGTGTGCCAGCACAGAGCCTTGGCAGCGAGTTTCACAATCAGAAGGAACTACCTGTAGGATACTCTTCTTTTATTGAGACGCAGTCTCACTCTGTCACCCAGGCTGGAGTGCAGTGTGGTGCAATCTCGGCTCAATGCAACCTCCGCCTCCCAGATTCAAGTGATGCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGCGCCTGCCACCACGCTTGGCCAATTTTTTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCTTGACCTCAAGTGATGCATGCATCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCCGGCCAGGATATTCTTATTTTGAGGCAATTTAGTCTGGTGGTTGATAGCTTAAGTGTCCAGAGTCCAGCAGCCTTTGCTTGAGTCCTGGCTGTACTGCTGCAGGCCTCAGTTTCTTCGCCTGTAAAACAGAGGCGGCATGACTGACGAGAGTATGGGAGGCGCCCGTGTTGCATCAGGATCTTCACCTCTTGTCAGTAGTTCCATTTGTGAGAACGTGCTCATGGGATACCCAAAAACTGTATTAGGGACATTTTTAGACCCATTTCAAAGTTCAGAGAGTCATTCATGCATGCGTCCTTAGGTGCTCATCCCCCACCTTAGTGGTTACGAACACAGGGCCAAACTTGTGTTCTGCCCCCTCTGTCCCGCTCTGCATCCCCCAAATTCCCGATGAAAGCATGCAGACATTCCTGGGGGAGTCCAGCTTTTGCTGAGTCAGGTCCACGTGGTCAGGTGGTAGTCTCGGGCCAGGCCTGTTCCAGGGGGGTGCCTAGCACTGCCAACCCAGTGCCCGTGGGCCAAGAGGTCGTCTACAGCAACTTCCCAGTCACCCAGCGTCCCATGTGCTGTGTATGTCACCTAAGCACATACTAGAAACATATAGGCAGCTAATTAAACTTTATTGCCAGTGAACACTGAAGCTGCATTGCCCGGCATTTTGAAGACGGCTCACTTGCCATCACCCGGTGGTGACAGGGGCCTTTGATTTTTGCCCGTGTCTAG
Seq C2 exon
ATGGCTTCCCAGTTACGACTCTTCGATCCCCAGCTGAAAGAGAAGCCAGAAGAGGAGTCCTTGGCCGCACCCACGTGGCTGGTTCACCTGCAGCAGGTGGAGCGGCAGATTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148396-SEC16A:NM_014866:18
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=0.105
Domain overlap (PFAM):
C1:
PF129312=Sec16_C=FE(17.6=100)
A:
NA
C2:
PF129312=Sec16_C=PD(11.1=76.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTTTAAGTTCATCTACTCCTGCCG
R:
CTTAATCTGCCGCTCCACCTG
Band lengths:
254-1531
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)