MmuINT0140492 @ mm10
Intron Retention
Gene
ENSMUSG00000026924 | Sec16a
Description
SEC16 homolog A, endoplasmic reticulum export factor [Source:MGI Symbol;Acc:MGI:2139207]
Coordinates
chr2:26409431-26412913:-
Coord C1 exon
chr2:26412836-26412913
Coord A exon
chr2:26410954-26412835
Coord C2 exon
chr2:26409431-26410953
Length
1882 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TGCTGTTCCTTTTGTTCTAGGCT
3' ss Score
10.29
Exon sequences
Seq C1 exon
GCTCCTGGAGACCATTGTCCTACAGGGGCCCCTCATGGTGGGTCTGTGCCCTTTTACAACCCTGCTCAGTTGGTGCAG
Seq A exon
GTGAGTGACCCTTGCCTTTGTTCCCCACAGCCCCAACTTTTCTGCTCAGTGAGTCTCCTTTGTTCCCTGGCTGGCTGTACTTTTGGGGGGGTTTGTTTTGTTACTTGTTTTTTTTAAAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTAGAACTCACTCTGTAGGTCTCTTACTTGACTTAGTCTGCATCCTATGCTTGCCTGCTGCTCCTCTCACTACTCTGGGCTCTTCAGGGTCAGGGATTGTTCTTTTTGTTACTTGCCATGGCTGAGGGTTGGCTCTCACTATTGCCAACCTCCCATTCCTGCACAGGATGCATGGTTTTCCCAGGTTAGCCATAGATCACAGGCTCTAAGCCCAGTCCTCTCCCTCCTGCCTCCCCCTCTTCTCCTTAAGAGCAGCTCTTCCAAGGAGACCCCTGGTTTGGGATTTTTCATTGCTTCAATTCCTCTGTCTGAGTGACACATTGTTTAATTGCTTGACTCTTGAAGATCCTTTGGGTCTGCCCTAGGTGCTGGGTTGAGAGTTTGCTGGGTGCAGTTTTTAGATCAAAAATGGTAGTACCATTTTCTGGTGCTCACTGTAAGAGAGTCCGGGTCTTCATTCTCTGTCTCTGAAGGCTGGAATAGCATCTTCCTTGAGGATCTGTACACCCCTTCCCTCAGTCATGGCTCTTGTGTTCTTCGCCTAGGAGAGTCTGGAATGTGCTATATAGTTTCTCTCCTCCACCATCTTTTGAAGAAGTATAGTCTGGCTTCTGTGGAGGGGACGAGCTCTAGGCAAGCATCTTTATTTTGGGGGACAAGGGACTTAAACCAGGTACTTAAACATGCTGCACAAGTACTCTAAAAAATGAGATGCAGTCCTGGGGAAAGCAGCATGTGTGGGGTTTTTGTTGTTGTGTTTGGTTTTGTTTTTAATCAAAGGGCAAGCAAGCAAAGTTTATTTAAATTTTTATTTTATGTGTATGGGTATTTTGCTGCATATATGGCTGTCTACTATTTGCATACCTAGTGTCTACAGAGACCAGAAGAAGACATCAAGTCCCCTGAAACTGGAGTTACAGATGGTTATGAGTCATTATGTGGGTGCTGGGAATTGAACCCAGGTGATCTGGAGGAGGAGTCATTTTTTTTGTTTTGTTTTTCATATATGTCATACAAAGTCTATTGAGAAGTAAATAAATCTTTGCAACCAGGAAGAGCTCAAAATGAGTTACCTGGGCAGGTATCTTGACATTCTGAATGTGATGTTCTCAGCCCACTCTAACAGGGACCCTGCCCGCAGCTGTGCTAGACCCAGCCTTGGCCACTCTCTGTTTAGTCCTCTTGAGGGGCCTGGGCCCTGTGCTAAGCCCTGTGCAGATGAGGCTGCTGATATCAACATTTTTGTCCATATTTTCAACTCCAAGATCTCATTTTTCTTTTGAGCTTGTGGTTGAATAGTTCTGACAGATTTCTTGGATTAGATCCCAGTAAGGTCTAGTGAGGGAGGAAGAATATATGCAGTGTTCTCTCGTGGCATGCAGCGTCCTTGTGCTTTCAGGAGTAGAAAATTATAGGCCACTGGCCACCCTTGCACTCAGTGAACCCTTAGCTGCCCCCCCCTCCCCCCCCCCCCCCCCCGCTCTGTAGTGCTAACTCAGCTCTTTTGACCTTGACAGAATTGGCAGAACAAAAACAAATCATGTCTGCAGTGCTGTGGGCTAGGAAATGCTGAGCAGCAGGAACTTGGCACATACAGAAGGTCTTGCTTACACTTGAAGCTAACACAGAGTCTGCCCATTTGTTATTGATCTGTGGGGTTATCCTGTAGCTCCATCGCTGGACAGCCTCTGGGCATGGACACATGTAGGTCATTGCTGTTCCTTTTGTTCTAG
Seq C2 exon
GCTTCTGTCACCTCGGGAAATTCAAGGCCAGGGAGGATTGGCCAAAGAAAATATGCGGCATTGAACTAGGATTGCTGCTGGATTCTTATTTGGAACCCTGAGATGATTAGATAACTGTTCTTCACCAAGAACCAACTAGCTGCCTCAGGTCTCGTGGATCCCAGATGGACATGGCAGTAACTCAGAGCCGGTCATACTGTGTGTCTCCTTCCTTGCAGCCTATGTATATGAATGATTGAAAAATTGATTTCAAGGTTCCTTTCAAATGCTGGATAGAATGAATCTAATTCAAAGTCTTTTATGTAAAAGAACAATGTTTCTTTTTTAGTCACTTTAGACAAATTAAGGTTTGAGCCACTTGAGAATATCCCCGCAGAGAGGCTAGGCAGGGATTCACTACAGGAGAGCACAGTTACTTGGACACCAAGGCCTTTCTCACCTGAGAAATGGTGCAAACCAACCAGGGATCCTTAGGCTACTGAGAAGGCTGTCTGCTTACCTGGAGAGGACTGACTGCTGGGATGTCTGGCCTAAGAGGAGCCTCAAACTGCACTGGGCAACTGTGCCTTGTCCTGTGAACTGGGGAGTACATGCCAGCTCCTCAAAGGGTCACCAGATGGCAGCGGCTCCCAGGCTGGGGAGGAAGTGGTTACAAGGGCATGTCTCTCCAACATTTCCAGCCTCACTCCATTTTCTGTGGCCTCATTAGTGCTGGGTGCGTTTTTTTTTTGCTCCGAGCTTTCCGTCATGGCTCAGTCACTGGGGAGAGCCCCAGGGAGCTGATATTCTGAAGCTGCTGATCTGATTAACCAGGTCAAAAACTGGCTGTGTGCTGCAACGTACTGCCCTCCTAGCCAGGAGTCTGTATGGAGCCCTCTAGCTGACTCAATGTCACCTGCAGACAGCACTTAAAGCCTTGGTGGTATCTTGGAGTGGCTTACGGTGTCCTAGCGCACACTCTGGAACCTTGCATCTCTACCCCAAAGCCCACCAGGGACCTTCAGCAGCGACTCACTGGCTCACCCATATCACTTCAAGGAGCTGCCACCACATAAGAGTCAAAGCTTTAAGGCTTCACTGACTGTTCCTAAAACTATCCTTACACTCTAAAGAGGAAGGGAAAGAGAGTTAAATATTTAAAAATCAGCAGGTAGAAAACATAAATGGTTTGTTTGGTATTAAATTTAGAAATTGTAGAACATGGAATTAGTACAGCCCTTCCCGGTTTTCTGGTTCCTTGCATCATCTAGGAAAGACTCACAGAATGGCTTCCAGGACGTTCCATAGATGAGTGTACTTGGACCCTCCTGTTCCTGTCATTAAGAAAGGCCTGTCCCTGTGGGTCAGTAGCAACTTGTGTCCTTGCTGGGACCAGGCAGGACCCTTGCCTCTGGTTCAACCCTGCCCAGGCTCTGTGTTGACTGCCAACCACTTTGGATTCAAGAAGCTTCCTCCCTGGGAGCTGCTATTTTTCCAAAATTCACATTGTTAAATAAAATATTTTGGGCTCTCAAGTAACTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026924:ENSMUST00000114082:30
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.981 A=NA C2=0.986
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GCTCCTGGAGACCATTGTCCT
R:
TCCAGCATTTGAAAGGAACCTTGA
Band lengths:
351-2233
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types