MmuINT0152761 @ mm9
Intron Retention
Gene
ENSMUSG00000068882 | Ssb
Description
Sjogren syndrome antigen B [Source:MGI Symbol;Acc:MGI:98423]
Coordinates
chr2:69699619-69701372:+
Coord C1 exon
chr2:69699619-69699796
Coord A exon
chr2:69699797-69701280
Coord C2 exon
chr2:69701281-69701372
Length
1484 bp
Sequences
Splice sites
5' ss Seq
AAGGTACGA
5' ss Score
9.78
3' ss Seq
AATAATAACCTTCCTACCAGTGT
3' ss Score
5.03
Exon sequences
Seq C1 exon
TGCGTCCGCGGCCACGCCCACCTGTCCGCAAGGGCTGCCGGGAAAGCCCCCATCTTTAAGCGCGTTTGGCTGGCCCGCCGGCGCTCGGAAGTCCAGGCGCTTCTGTCGTTGTTCTTGAAGCTGTGGTGACCGTGGGATCCGAATCTTTGAGGTGAGCTTCTTGGAAACTGAGGAGAAG
Seq A exon
GTACGAAGGGCTGTGCTATGCGCAGGCCTCACCTTCCTCTCCGCGCCGCCGCGTGGGCCGCGCGGCCCGTGGCCGTGTGCTGGACCGCGGCCCGAGGGGGCGCGGGCCTCGGCGAGGCCACGGAGCGGGCCCCGGCCAGAGATGCGGGCGCCTGGGGCTTTCCACGTGGCAGGGATCCCGGCGGGCCGGTGTGGGAGGATGCGGCTCTCGCGGGGCCTTTAGGCAGAGGCTCGCCGCATCCTCACGGCGTCCTTTCGGTTTGTTCCTTGCACCCCTTTCCTGACTGGCCAGAGGCGGATGTTTCGGACCATTTAAGTCTTTAGGGTGGTCGGTGCGGGTTAAACGCGACAGGGTTCTGTGGGGACTGACTGGAGGCCGAAGAAGTGGGGGCCGCTATTGGGTTCCCAGCGTCGCTATCTTTTTTTTTTTTTTTTTTTCCTTCAAAGAACTGCCATTGCCATTCTGTCTTCAGTGTGAAACAGTCCCTAAATTGGGTAGGCCGCAGAAGTCTTGCAGGGGCTAACTAGGTCGTTATTGACCTGTGTCTCTGTAGTAATGAGAAGTGAGATTGTTGGTAGTGGGAGACAAACCAGCGCCTGTAACAGTAAATTCTGAAGTGGGACGTGTACTTCGTAGATTTCCCATTACAGGACCAGTGTATCGCCAGCAGTCTCCAGCATTTTGAGCAATGTCTCAAGAAATATACCAACAGTAACTCATAACTATATTCAGCTGCTGCAGATAAACTCTTCAAGAGCTGGTATACTTCCGTACAATATGGTAGGGTGGTTTAGTAAGGCGCTGAAAGCCAGTAAGACAGAAGATCCGGTTTGTGATTTCTAGCAAACCAGTATCACAGTCCCTCTTTATTCTAGGATTGTTGTCAGACCGTGAAACAGGAAAGTGGCTATAGAGTTAACCAGTGTAGTAGTGTTTTAGGCACATCCTTACCTTCCAGCGTCCCTAGTTTAAAATTTTTTGTATCTGTGCTCACAAGGTCCCATTTTTCTTGTATTCTCCTATATAGTGTCTAACACCGTAACTTTCATATCTGAACTCTATTTTCATTTTTACCAGTAATAAGTTTTGGTAAGTCAGCTGTGACTAATTTGAAAAGAAACGCAAATAATTGGCATTGAGGGCTATAGGAATATACTGCTGGCAGACTATAATACTGATATTTTTAAAGCTAGAAATGATTCAGGGGTAGTTAAGTGGACATTTTCTGCTTTTTTGTTTTTATCGCTGAACTTTGCTTTACCAACTACATGAAGAGTTTGGTTACAAAGTAGGATTTACTGGGAGGAGGGGTTGTTGATCTGAGTTTTCCATCCATAATCCAAGGTGTTGCTTTGTTGAGATGTATGAGAATTCATAGGGAAACCTGTAAGGTTAGGAATTCTTGAAATTAAAAAAAAAGTGGCATACTTTTTACTCATTCTCTTGTATTGACTATTATATAAAAATAATAACCTTCCTACCAG
Seq C2 exon
TGTGAGAAACTTTACAGATAGCCACAATGGCTGAAAATGGAGATAATGAAAAAATGACTGCTTTGGAGGCCAAAATCTGTCATCAAATTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000068882-Ssb:NM_009278:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.273
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0538312=La=PU(8.5=22.7)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGGGCTGCCGGGAAAG
R:
ATTTGATGACAGATTTTGGCCTCC
Band lengths:
238-1722
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: