HsaINT0146705 @ hg19
Intron Retention
Gene
ENSG00000148396 | SEC16A
Description
SEC16 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:29006]
Coordinates
chr9:139334548-139338352:-
Coord C1 exon
chr9:139338275-139338352
Coord A exon
chr9:139336276-139338274
Coord C2 exon
chr9:139334548-139336275
Length
1999 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TGCTGTTGATTTCATTCCAGGCC
3' ss Score
7.14
Exon sequences
Seq C1 exon
GCTCCTGGCGACCTCCCTGCTGCAGGGGGCCCTCCCAGCGGGGCCATGCCCTTCTACAACCCTGCTCAGCTGGCACAG
Seq A exon
GTGAGTGACTCCTACCTTTCCCTACGAGACCCTAACACGCCCACTGACGACCTGACCCTGCTGCTCAGTGATGGCAGCTTTCTGCCCTAGATCCTCTTTTTCTTTCTTTTTAAAAAATATATTTATTTATTTATTGAGACAGGGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGTGCGATCTCTGATCTCAGCTCACTGCAGCCATAACTTCCTGGGCTGAAGCAATCCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGCATGGTCAGCACACCTGGCAAATTTTTTATGTTTTGTAGAGACGGTCTCACCTTGTTGCCTAGGCTGGTCTTGAACTACTAGGCTCAAGCGATCTTCCCACCTCGGCTTCCCAAGGCACTGGGATTACAGGCTTGAGCCACCGTGCCCAGCTTCTCTTTTCTGAATGAAAGTTGCACACCTACTGGGTGGCAGTCCACAGGGCACTGTGAGGAGCCAGGCTGGGCCCTCCCCGGCTGCCATTTCTCCCTTTGTGTGGACACCAGGCCCACCGTGCTCAGCTCTGCGTGGACACCAGGCCCGCCGTGCTCCCGTGTGGAGCTCTGTCGACACGAGGCCCTCCGTGCTCCTGTATTCGCTTTGCCTTTTCCTAGGTTGTAGTTTGTAAAATGTGCTTGGCTTTCTACTTGTGTATCCCTCATTCAGCCCCCAGCTCTGCCACGTCTGCTATTCTGTTCTCCTGGAGCCCGTGGTCTCTGAGCCGAGCGTGATCTCTCCTCCCTTGGCCCGGGCACCCGGGTCTCCCCGGAGTGGGTCCCCCAGCTTTGGAATCCTATGTTGCTGCCTTTCTTAGTTACTCTGTTTGTCTTGGTGACACACATCCTCTGGTAGCTCTTGCTTTTTTTGTATGTTTTTTATTTCTTTTTCCTAATAGCTTCTTGACAGAAAGGTCCCAGGGTGACTTGGGAGATGCCTTTCACGTCTGGAGCTGCCTTTCTCCTCCGGCCTATCTGGCTGGCTGGTAGAATTCTTGGGCCAAAGTCACTTTCTTCAGAACTGCAAGTGGCCTTAGGTTTCCTGCTGCCTGTGGTTGCTGAGACCCCAGGGCCGTTCTGCCTGCAGCCCCTTTCAGGGTCCGTTTCCCTGGGACCTGGAGGGCTTCACCCTCAGCCCCCTTGGGCCTGACTGCATGCCCTTCAGCTGGGGAGTGTTCTAGAATGTTTCCTGTGGTTTCCCTCCCTCAGCCTCGTCTCTCCTCCCCTCTCCCTTGCCTGTGGAGTATAGACTGGCTGCCAGTGTAGGGGAGCTGAGCGGGGTCCAAGGTCTGGGGCCTCTTGGGATTCAGCCCCATTGTCACCCCAGCCTGCCCTCACAGCCTCACACACTCTTGACTGCAGGCTTCCTGGGCTGGGGCCCAGCACTCCTGCCCTGGTCCTCTACAAACGAGGCCGAGGCTCCCAGGACCACTGCCCCCAAGCTGGCCCCTGGCTGTCACCTGCTTTTCAGCATCCAGACTAGTCGATTTTGGTATTGTCCTGCTCCCTTTACCATGTGGTTAGTGCCTTTACAAAAATTCCTTGGCTTTCCCCTCCATGAGGCTTTGCGAGGGAGCAAGAGTGGATGCCTGCATTGGCCAGCTGTCTGCAACTGAGGTCCCCGCGTCCCATGCAGTAGGCCAGGCCTGGCCACCACTTGTCCCTGGACTCTGGACAGCCAGGCTGGCTCTGCAGAGCAGCTCCAGGTCTCATGGCCCTGATGAAACCACGGCACCTCCTGGCCACCCTCACAGTAAACATTGATGGTTAAGGATACAGTGCTTTCAAGGGAGCCCAGGACTTGGCACTGACTTGTCGGTTTCCAGAGGCTTTTGGAAACAAAAACGAAGCCTTCAGCTTGTCAGCGCCAATGGCCCGTGTGGTTCATTATGTGGACCAGCCCCTGCCACGCTGCAGCCGAGCACTGCTCACCCTGGGGGCAGGCATGCAGAGGTCATGCTGTTGATTTCATTCCAG
Seq C2 exon
GCCTGCGCCACCTCCGGGAGCTCAAGGCTAGGGAGGATTGGCCAGAGGAAGCACCTGGTGCTGAACTAGGCTTGCCCTGCTGTGAACTTGCACTTGGAGCCCTGACGCTGCTGTTCTCCCCGAAGAACCCGACCGACCTCCGCGATCTCCGTCCCGCCCCCAGGGAGACACAGCAGTGACTCAGAGCTGGTCGCACACTGTGCCTCCCTCCTCACCGCCCATCGTAATGAATTATTTTGAAAATTAATTCCACCATCCTTTCAGATTCTGGATGGAAAGACTGAATCTTTGACTCAGAATTGTTTGCCGAAAAGAATGATGTGACTTTCTTAGTCATTTAGGATGATTTAAGGATATAGTATTCCTGGTCATTTAAGAATGTTCATTCATTGAAGCCGGAGCTGTCTCTGCCACAGGAGAGCCACATGGTCGGTAGTAACCAGGGCCTCTCCAAGCCCAGCTGTGAGTCACTGCCCAGTGAGTCCCGCGCTTCCTTTAAGGTGCTGGGAGCAAAGAGAGGGTGACTGAGGCAGACCCCAACCCCTGCTCTGCACCATCTGGGCCCTCGCCGTGTTTGAACCTGGCTGAATGAGTGGAGGGCGCTGTGTTCTCAATCAGCGCCTCCGAGGAGCCGTGGGGTTCCTTCGGCATTAGTTCACGGTTTTTGAGAGAGGCCTTAGTTACTGCAGTGAATTTCTTTCCTGTTGCAAAGACGCTTCCAGCCTCACTTTACTTTCTGTGGCCTGATGAGGACCATGGGTGATTTTGTGTACCCAAAGCGCTGGGGACTGCCCACCGTGTGGCCCAGTCACTGGGAAGGAGCCCCAGAGAGCCGGCTGTCTGACATGATGGCTCAGGGTGGTCATCCAGGTTGAAAACTGACCGTGTGATGTTTGATTTGGGCTTCATTTCGTGTGTAGGAGCACGGTTAGACTCACTGTTAAGGAAGCTGGATGCACTTCTCTAAAAGGCTGCACTTTCCGTGAGCACTTTTCGTGGTACAATCCACATGACCCACTTTCTCCCCTGGGGGACGTTGGTTCAGAGGTTGGTAGCACTTGGGGAGAGTATCTTAACACAGTTTCTTGACAGCAGCTCTGGAACTTAGTATTTCTGCCCCGAGTTTTGCCACACTGAGACTTTGAGTAGCTCCTGGTGGACTCAACCCTGTTCAACTCAGAGACGGGCCTCCTCTCACTGATGCAAAGCTTTAAGGCTTCTCTGACTGTTCTGAAACTCTTCGTATTCTTGTCAAGTCTAAAGAGACTGAAGAAAAGATTTAAATACTAATAAAAATCAGTAGATAATTTCTGTAGGTTCTGCTGGAGGAATACAAACTGTTTGGTGTTTTAAATTTAAGTGTAGAAATTGTAGAATGTGGAATTAGCACAGATCCTTCCTGGCTTTCTGTTTCACTTGATCATTTAGCCCAGACCACCCAGGATGTTTTCCAAAATGTTCCACAGGCGTGTCCCGCTGGATCCATTTGTCCTTGTCACTTGGAGAAAGGCCAGTCCCTGTGACGGGGCAGCCCTCTCTGTCCCTCGGTCAGCTCGTGTGAATCCTGGGACCTCTTCCGGTCGGCTCTGCCCGCTGTTCTGGGGTCGACTGCCACGACTTTTGATTCAAGAAGCTTCCTCCAGGCGGGAGCGGCTATTTTTCCTAAATGAGAATTGTTACATTGCAAATTGTTGAATAAAATATTTTGCGCTCCTTCAAGCACCTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148396-SEC16A:NM_014866:31
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.992 A=NA C2=0.923
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CATGCCCTTCTACAACCCTGC
R:
TCGGCAAACAATTCTGAGTCA
Band lengths:
344-2343
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)