MmuINT0140513 @ mm9
Intron Retention
Gene
ENSMUSG00000026589 | Sec16b
Description
SEC16 homolog B (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:2148802]
Coordinates
chr1:159489580-159491107:+
Coord C1 exon
chr1:159489580-159489652
Coord A exon
chr1:159489653-159490813
Coord C2 exon
chr1:159490814-159491107
Length
1161 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCT
5' ss Score
8.16
3' ss Seq
TGCTGCTGCTTCTTCCTTAGACA
3' ss Score
7.95
Exon sequences
Seq C1 exon
CAAAATAGAACAGGAGCCCCGAGAGATCCTGATTCGACTCCTTCAGATATTTATGGAGCTGGAGGAACAACAG
Seq A exon
GTACCTAACATGAGATCTGATTACCATAATCTGATTGAAATATCTTCAGCTGTACCCACACTTCCTTTTCTTTGGTGCCTTCTTCTTCTAGGAATTAAACCTGTTGATCCAGGCTGCCTCTTTTGATAGGCCTTTGCTGGTCTCATAGACCCTGGACACATCCAAATTCCCATAGCATGAGGGTTCCTGCCCTGCAGGCCAGGTTTTCCAAATACTTGATTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTACTGTTAGCTAATTGTTTTACCTGTGTGCGTACTTGCTCCCAGCTAGTTTTCTTTCTTGTGCCCAGAGATTACACACCATTAGCATCTTTAGTAGTGTCCTAGACATTGGAAGTGTGAAGATGTTGAGCTATCAGTTGGTCATGTAACTGAAATCAGTTTCAAAGTGTTTGGTCAGTCTCCTCCCTCAGATTGCCTCCAAGTGTCTGGTCAGCAGGAATTGTATTCCAAATTAACTCCGTACATTTCATCAAAGCCATCCCCTAGGTCACGGTGAAGTTCAGACAGGATCCCCTGTCTCTTGCCTTCCAGCCTTTAGTACTTGCTTCCTGGATGGGCAGAATGGAGGGAGGCTTTGGCTTCTGTTCCTTGGCTTTGTGTGAGCTTGGCTGGGCATCTCTATGTGATAACGTTCTTACAGCCCCGGCAGGAAGGCTGGCAGCTCACAATATTCCTGTGTCCGGGAGCCAAGCATTTCACACACCCACACCTTCGTGGATGTATCAGCCAGGTCCCTTCCAGGGCAAATGAATCCAGACTCTTCACAAGTGAAGCCATCATCTCTAAAGTGTCATTTGAGTTTTTAACTGTAAGTTTTAAAAGTCTAACGAAGTCCCCTTAAAGGAGAATGTTAAAAGGTATAGAGTTCAATTGGATGTCATTTCTGTCCTCTCCACACACAGGAGTAGGGCTCAGAGATTATCCAAGAAGTAAGAGCGTAATTCTGAAGAATGCAGAGAGAGAGGTGTTATGGTTAGTCAGTGCTTTGCCTGCTATCAAATTAATGGAAGCCACGTGTAACAGCCAGCCCGTGGGATTGCTTTCTAGAGAAGACAAGAGCGGCAGTGTTTAATGGTTTGTCTAACTGCTGCTGCTTCTTCCTTAG
Seq C2 exon
ACACTCCCTACCCTGATCTCTCTGGCCATCAAAACTACTCAGAAGACTCTGAGTACAGCTCCACCTTGTGGTCAACAGCAGAGCAGACAAGCCTGACCAATCCCCTCGCACAGCAGTCTTTCCCCCTGCAGCGAGATACCTATTCAGGACACATGGGAACCCCAGTGCCTCTCTACTCAGTTCCTGCAACCCACTTGGCAGTGACGAGTGGAGCCAGTGGTAGCAGTGTGGCAGTGACGGGGACTCCTGGGGGAAGGGTTGGAGAGGATATGCTGCGGACACATCCTGCCTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026589-Sec16b:NR_027641:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.984
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATAGAACAGGAGCCCCGAGAG
R:
TCCGCAGCATATCCTCTCCAA
Band lengths:
348-1509
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: