MmuINT1032221 @ mm10
Intron Retention
Gene
ENSMUSG00000068882 | Ssb
Description
Sjogren syndrome antigen B [Source:MGI Symbol;Acc:MGI:98423]
Coordinates
chr2:69861562-69863315:+
Coord C1 exon
chr2:69861562-69861712
Coord A exon
chr2:69861713-69863223
Coord C2 exon
chr2:69863224-69863315
Length
1511 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
AATAATAACCTTCCTACCAGTGT
3' ss Score
5.03
Exon sequences
Seq C1 exon
TGCGTCCGCGGCCACGCCCACCTGTCCGCAAGGGCTGCCGGGAAAGCCCCCATCTTTAAGCGCGTTTGGCTGGCCCGCCGGCGCTCGGAAGTCCAGGCGCTTCTGTCGTTGTTCTTGAAGCTGTGGTGACCGTGGGATCCGAATCTTTGAG
Seq A exon
GTGAGCTTCTTGGAAACTGAGGAGAAGGTACGAAGGGCTGTGCTATGCGCAGGCCTCACCTTCCTCTCCGCGCCGCCGCGTGGGCCGCGCGGCCCGTGGCCGTGTGCTGGACCGCGGCCCGAGGGGGCGCGGGCCTCGGCGAGGCCACGGAGCGGGCCCCGGCCAGAGATGCGGGCGCCTGGGGCTTTCCACGTGGCAGGGATCCCGGCGGGCCGGTGTGGGAGGATGCGGCTCTCGCGGGGCCTTTAGGCAGAGGCTCGCCGCATCCTCACGGCGTCCTTTCGGTTTGTTCCTTGCACCCCTTTCCTGACTGGCCAGAGGCGGATGTTTCGGACCATTTAAGTCTTTAGGGTGGTCGGTGCGGGTTAAACGCGACAGGGTTCTGTGGGGACTGACTGGAGGCCGAAGAAGTGGGGGCCGCTATTGGGTTCCCAGCGTCGCTATCTTTTTTTTTTTTTTTTTTTCCTTCAAAGAACTGCCATTGCCATTCTGTCTTCAGTGTGAAACAGTCCCTAAATTGGGTAGGCCGCAGAAGTCTTGCAGGGGCTAACTAGGTCGTTATTGACCTGTGTCTCTGTAGTAATGAGAAGTGAGATTGTTGGTAGTGGGAGACAAACCAGCGCCTGTAACAGTAAATTCTGAAGTGGGACGTGTACTTCGTAGATTTCCCATTACAGGACCAGTGTATCGCCAGCAGTCTCCAGCATTTTGAGCAATGTCTCAAGAAATATACCAACAGTAACTCATAACTATATTCAGCTGCTGCAGATAAACTCTTCAAGAGCTGGTATACTTCCGTACAATATGGTAGGGTGGTTTAGTAAGGCGCTGAAAGCCAGTAAGACAGAAGATCCGGTTTGTGATTTCTAGCAAACCAGTATCACAGTCCCTCTTTATTCTAGGATTGTTGTCAGACCGTGAAACAGGAAAGTGGCTATAGAGTTAACCAGTGTAGTAGTGTTTTAGGCACATCCTTACCTTCCAGCGTCCCTAGTTTAAAATTTTTTGTATCTGTGCTCACAAGGTCCCATTTTTCTTGTATTCTCCTATATAGTGTCTAACACCGTAACTTTCATATCTGAACTCTATTTTCATTTTTACCAGTAATAAGTTTTGGTAAGTCAGCTGTGACTAATTTGAAAAGAAACGCAAATAATTGGCATTGAGGGCTATAGGAATATACTGCTGGCAGACTATAATACTGATATTTTTAAAGCTAGAAATGATTCAGGGGTAGTTAAGTGGACATTTTCTGCTTTTTTGTTTTTATCGCTGAACTTTGCTTTACCAACTACATGAAGAGTTTGGTTACAAAGTAGGATTTACTGGGAGGAGGGGTTGTTGATCTGAGTTTTCCATCCATAATCCAAGGTGTTGCTTTGTTGAGATGTATGAGAATTCATAGGGAAACCTGTAAGGTTAGGAATTCTTGAAATTAAAAAAAAAGTGGCATACTTTTTACTCATTCTCTTGTATTGACTATTATATAAAAATAATAACCTTCCTACCAG
Seq C2 exon
TGTGAGAAACTTTACAGATAGCCACAATGGCTGAAAATGGAGATAATGAAAAAATGACTGCTTTGGAGGCCAAAATCTGTCATCAAATTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000068882:ENSMUST00000090852:1
Average complexity
IR
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
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGGGCTGCCGGGAAAG
R:
TCAATTTGATGACAGATTTTGGCCT
Band lengths:
214-1725
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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