HsaINT0159322 @ hg19
Intron Retention
Gene
ENSG00000138385 | SSB
Description
Sjogren syndrome antigen B (autoantigen La) [Source:HGNC Symbol;Acc:11316]
Coordinates
chr2:170655389-170657536:+
Coord C1 exon
chr2:170655389-170655486
Coord A exon
chr2:170655487-170657461
Coord C2 exon
chr2:170657462-170657536
Length
1975 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TAATTTGGGAAATTTTACAGATA
3' ss Score
3.4
Exon sequences
Seq C1 exon
GGAGCGCTTTAGGCTGGCCGGCGGCGCTGGGAGGTGGAGTCGTTGCTGTTGCTGTTTGTGAGCCTGTGGCGCGGCTTCTGTGGGCCGGAACCTTAAAG
Seq A exon
GTGAGTAACTCTCGGTGGCTAATGAGAAGCTACAAAAGGGTCCGCTTTGCTGGTGCGCGACTGCGCGTTTCCGTTCTTTACTGCTTCTCGCGGCGTCCGTCCGCCCCTCGCCTTCCTCACGTTCAGGCCGAGCGCCGCGTGGGCCGCAGCCGGAGGCGGCGGAGCCGAGGGGGCGCGGGCGGCGGCGAGGCTGCCCCCGCGAGGAATGCGGGATCCTGGGGTTCCCCGCACGTGGCTGGTGCCCAGGCAGTTCCGCGGTTGCTTAGAGACGGGACTGTGGCTGCCCTCATCCCCATTGCGTCTTTTTTTTTTTTTTTTTTTTTTACCTCCACCGCCTTCTAGTCTCACCGAAGGCTTGTGGCCATCTCTGTAAAGTTTCTGGGGAGGTGGGCACGGGGTAAACGCCGGAGGGTTCTGTGGAGCCTATGGGACTGACTGGAGGCCAAAGAACTTTGGGCCGCAGATGTACACCAGCGTCACTCTTTTGGTCTGTTAGGGCCTTCATCGCTCACATCAGGTTTCAGTGTGAAACGGGAAAACGTGGGTAATATTTCATTTACAGTCGTACATTCTGGAAAAGTATCTGATGAAACGCAGTTCCAAAATTAGGCCAAATAGGTTTTGCAGGGTCTAAATAGTTATTTTATTTCATCGTTTGCTTTGTAGGGGGCCCTAGATCACGGTAGTAACTTAGGAGTGTAGATTGTGATAGACAAGACAATGCATAAAATTGAGTAATTTCTCTAGGGGGATGTGGATCACACAGTACCCCGTTGCAAGTGCTTCCTATGTGTATCCATGGTATCGAATGCAATTGCAGTGTGTCAGGGGATGCTTCCAGGAAGTGTACCTACATCAGTTCATAACTAGAGTCAACTAATGGCAATATTCTCGATGATTTGTTCACATAACTTTTGTACAGTTGGGATGACTGGGTGGCTTAGTAGAGTCCTGGAGGCAAGTACTTTGTAAGTAGAAGACTTGGTTTGTAATTTCTAGCAAACTAATAGCACAGCTTCCTTTTTTCATTGCAGTGCTAATGTCAGGAATACGAAACAGGAAACTGGCTATCCAATGTATTAGTAAATTAGTAGGCATACTCCCCAGTTTAATGTTGTGTTAGTATGACCACATTCTCCCATTTTTGTTTTCGTATGTTCCTTAGCATAGAGTATCTAAGGAACTGTAACATTTTTCACCTTAAAGTTATGATGTCTAACTTGGTAACAAGGTTTGGGTAAGTCAGTTGTGACTACATTTTAAAAGAAATGAGGCCGGGCGCGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCGCCAGAGGTCAGGAGTTCAAGACCAGTCTGACCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGTCAGCCGCAGCCGTGGTGGTGGGCGCCTGTAATCCCAGCTACTCAGGAGGCGAAGGCGGAATCGCTGGAACCTGGGAGGCAGAGGTTGCAGTGAGCCGAGATCGCACCATTGCACTCCAGCCTGGGCAACAAAAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAGAGGTGAACCCATACCAAACAAATGCACAGAGAGCCATGGTAATATACAGATAGATAGTTATCTGTTTAAAACTGGAAATGGTTGGTAAGTGATTGGAGTTTTTTTCCCTAAAGCTTGCTTGACCAGCTAAGTGAAGATAAACAGTTTCTTGTTATAGAAGATGGGGTAGTGATTTACTGAAAGACAAGTTTTTTATAGTTTTTAGATTTTTTCATCACTTATTCCAAAGTGTTGCTTTGTTGAGATATTTGAGAACTGAGTAAAGAAACTGAACCCGTGAAAATAGAAATTCTTGATTTTTTAAGAAAACGGGATATTAATACTTTGTAAACATTATCTTTCTATTCTTGAGTTTTATATAAAAAATAACTTTATGCTAATTTGGGAAATTTTACAG
Seq C2 exon
ATAGCCGCAATGGCTGAAAATGGTGATAATGAAAAGATGGCTGCCCTGGAGGCCAAAATCTGTCATCAAATTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138385-SSB:NM_003142:1
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
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)