MmuINT0140522 @ mm10
Intron Retention
Gene
ENSMUSG00000026589 | Sec16b
Description
SEC16 homolog B (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:2148802]
Coordinates
chr1:157529164-157531392:+
Coord C1 exon
chr1:157529164-157529504
Coord A exon
chr1:157529505-157531279
Coord C2 exon
chr1:157531280-157531392
Length
1775 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
CTGTCTTTGTGATATCTCAGGTC
3' ss Score
7.95
Exon sequences
Seq C1 exon
GAAATTAAAGTAACTACATAACAGCCTCAAGACCCAACGGGGAAAATCAAAGGGCCAGAGATGGAACCTTGGGTTCCCCAGACACAAGGAAGGACCACGGGACCATCAAGGGATACAAATAGAGGACTTCAGAGTGGACATTATAGACCCCGTCTGCATTCTCAGTACAGTGGAGATAAGTACCACCAATGGCAAGATGCCCACAAGAACTCAAAGTCACAGCAGGACCTCAGGGATGACCACCAACAGTCTCACTCTGTATCCAGGAGTGGGGAGTGGTCCCAGCCTGTGTCTGGTGCTGACTACTTGAAAGGATCTTATCCCAGTCACCTGTACTCAAG
Seq A exon
GTATGATGCTTAGGGTTACAGTGAACCTATCTCTCCTGTGAAGAGGTTATTAATTGTTCTTGTTTCTTGTCCATTTCCTTTTTCCTCCCTGCCCCTCCCCCTCCACTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCCTCTTCTTCTTCCTCTTCTTCTTCCTAACTGTTTTGGTTTTAGGGTTTTTATTGCTGTGATAAAATACCATGGCCACAAAACCAGCTTGGGGAGGAAAGGGTCAAAGGGTTGTTACATCTTACACTTTCACTTCACAATCCATCACTGAAGGATGTCAGGGCAGGATCTTAAGTCAGGAACCTGGAGGCAGAAACTGAAGTAGACCACGAAGGAATGATGCTTACTTTCTTGTTAGCCCTGAACTTTTCTTTCTTATTCAACCCAGAACCATCTGCCAGGGGGTGGCACCACCCCAGTGGTTTGGACCTTCCCACATCAATCATCAGTCAAGAAAGTGCTCTACAGACTTGTCTACAGGGTGATCTAATGGAGGAATTTTCTGAATTAAGATTCGGTCCTGTCTAGATTTGTGTCAAGTTTGAGAACCACCAAGACACCCTTAGATAAAATCTGCCTTGCCTGATTTGTGTTTTGGTGACTGGTGACAGTGTTTCCCTCTTTTTTTTTTTTTTTTGTATCCCAAGCAGAACTTCATATAGCTGCCATCATAGAGTGACTGGGATGGAGGGATGGATGGATGGTAGAGAGACAAGAGAACAGATGTTACCTCCATGCTTTGTGATTGTAAAAGGCAGTCTTTGTGGGCTGTGGCAAAGCTTTTCCTAGGATCTCATGAAAGGCTTCACATTTTCACTGATCTTAGCTGGATGCCAACAGCACCAACAACCCCAGCATCTCATACTATGCCTGGAGGTGACAGACATGCAAAGATCAGTATCTAATCCATAAGAACTTTAAGAGAACTCAATTTCAGAGAAGGCAAATACAGATTTTCAGGCTATAATGTGAGGAGGAAGAGACCACAGAGGTAACTCTGTGTCAGAGAATCTTGAACTCTTGCTCCCCCAGGCCCATAGTATTGAACTAAATATTTCATGCCTTCCTTCATGTCTTCTAGTTGGGATTATATCTATCTGCCCTATGGTTTGAAGGTTAAAGTTATAGCAATTATTATAAAGAAACTTGCCTCTGAGGTTATTATTAATTGACAGAAACACTAATAATGTTCTTTTTCCCCAATCCTTTTGGGCCATTGAGTTCTCAAGAGGAATGAGAATGTCAAGGACAGAGATAATAAAGGCAATCACGCTGGTGATAGTATTCCGTCTGTCTGTAATGTGCATTGAAATTCCAGTGGCTCATGGCTCTTCTATGCTTTCCTCAGGAAGAGCTTTTTCTCAGATAATCCCAGGGGTGCCAAGATAACAGCTTTGATGATATTACATGTGCATATTTGTAGAATGAGAATATTGCTATAAAAACAATTGTAAATAAATTTCTCTTAATATTTAAAAGTGAAAAAGAGCTTTATTATGAAAGACATCCTTTTTTTTTGTAGAGCAAAGGGCCACCTCTGTTCTGATTTTGGATTTTCTGAATTAATGTGGCAGATTTCTGACTTAATCAGGCAGATTCTGGACTAGGCAGTCGTTCTGTCTTCTGAAGTTGTCTAGTTCATCCAGTCTCCTTTTGGTTTTGGCTGTCTTTGTGATATCTCAG
Seq C2 exon
GTCAGGCTATGGGGACCCCTATCAGAGGTACCACACTCCGACACCGAGGGATGAGTATGCTTATGGAAATTACTACTACCACGGACATCCACAGCTGCTGCCGGAAGAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026589:ENSMUST00000027881:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.926 A=NA C2=0.897
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAAGGGCCAGAGATGGAACC
R:
ATACTCATCCCTCGGTGTCGG
Band lengths:
352-2127
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