DreINT0156163 @ danRer10
Intron Retention
Gene
ENSDARG00000029252 | ssb
Description
Sjogren syndrome antigen B (autoantigen La) [Source:ZFIN;Acc:ZDB-GENE-030131-223]
Coordinates
chr6:3560182-3562198:+
Coord C1 exon
chr6:3560182-3560289
Coord A exon
chr6:3560290-3562094
Coord C2 exon
chr6:3562095-3562198
Length
1805 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGA
5' ss Score
6.91
3' ss Seq
ACTGTTTTTGTTCTCTGCAGGGA
3' ss Score
12.02
Exon sequences
Seq C1 exon
AAAGGCTTTCCTCTTGAAACTACGCTGGATGATGTTAAAGAGTGGCTTGCTGATAAAGGCACATTTGAAAACATCTACCTGAGGAAAGGACCCCAGAAAACCTTCAAA
Seq A exon
GTAAGAGTTGAACAGAGTCTAAGTGAGCTTAAACGGTGTTCGCTGGTCTTAAAAAATATTAAAAGTTAATAAATCAATTCAGAGATATTTAGAGAGGGTGCTCGCTGCAGAGCCATTTGAGCAGAGCTGAGCTCCAGCGAGGGGGAGCATGAGCTCTCGCTCTGCCTCCTGTAAGCTGTTTTAATGCGTACACCAACCCCACCCCTAACCCTACCCCCAGTGACATCACTCGTAGAAGTGCAAAAAAGTGGAGCTCAAGCTCCCCCTCGCTGGAGCTCAGCTCGCCCAAATGGCTCTGCATTGAGCACCACTTGGATATTTAAGGCCCTTAAAGTTTTAAATGCTACATTAAATGCCAAGGGAACACTATTATTCATGCTGATCTATAGGCACCACCCTCTGGATTAGCTTTTTGTTATTTATTATATGTATCATCTTTTAGTTTTGGATTAGTTTCTTACAATCAGTATTTAGAGAATATACTGTAAGTTAAAATGTCGCCAACGTTACCAGTTGAAACCTAAAGTGACAATGAGGTCTTGATGTATGGAAAGAGTCTTAAAGGTCCTAAAAGGTAGTGGATTTTTCTTTCTGAAATGTACAATGTTTATTTTGACAGCACACATTGTTATTCTTTAGATCAGTGGTTTTCAAAGTGGGGGTTGGGACCCCCCAAGGGGTCGCGGGACAATGAAGGGGGGTCGCCTGGTGATTTCCAAAAATCTGTTTTTTTATATTAAACCATAAGAATTACCATATTTTAACAATAAACTACTGAAGAGAAAAATTGTTGCATGCAAGGTTTCTGTGTATATATAACCACCTTAGAGGATATTGGGGATCGCGAGTCACTAGCATTGTTATTTTGGGGCTCGCAAGCTAAAAAGTTTGGGAACCTCTGCTTTAGATGAACAACTGCTCCATGTTAATCCACTGAAATATTTTTTAGGTGAAATCTTTAATCAAAGGCTGACCTGGAGTGGCGCTCCTTCAGTCCGACGGCTTTAGCAACAGTATTCTTAACCACGCCCCCTTACTGTTAATTTGCTATGCAGTAATGATGTGCATAGAAACCACTCAATATTCAGTTTAAGTTGGAAGAAAACAACATACTTGAATAAAAGCCGCAGTGATTTAATTGAGAACACATGATTCTGAAGATGCACAGTAAACATCCATACAATGCGCTGGGTTTGGACCGTTTGGTGGTTCAGAGACAATGGAAACATGAGCTACATTACGGTTGTCGTTGTGAAGCATTGTTTAGGAGTTTGTTCTTTATACGTGGATTACTCCATTAGCTAGATTTGGTTATTGACGATTTGACACAATCTAGGATTGTTTCGTTCTTCAAAACCGATCAGAGAGTTGTTGTCATAGCAACAGTTCTGGTAGCTCAAACCTGCTCGGGAGCAGCAGCTTATTTCATATAAACAGGATTAGAGCGGGTCATTTCAAGCAAAGGTAATGCTGGAAGTATGTACCAAATGCTAATACTTTCTCACAGTAGTAACCTATAGATTATATACATTTGGTGAAGTAGTAAAATAGTTTTAAAAAGTTATATATATATATAGAGTTTGGTGAACAGATGACCTTTACAGCCAATCACAGTGATTTCTGTTGAGCATGTGAACACAATGGCAAATCATAGCTTTTGAAGAACATGCTCAACAGCGCTCAAATGTTAGCATGAAATTCGATTAGTAATGAATTCCAGTATCGTGACAACACCAATGTAGCTTAACAATATTTGAACACTAGTTTTGTTTTTGTTTTTAGTTCACTGTTTTTGTTCTCTGCAG
Seq C2 exon
GGATCAATCTTTGCTGTTTTGGAAACTGAAGAAGCTGCCAAGGCTTTTGTCGAGCGTGACGACATCAAAAATTTCAAAGGAAACGAGATGATCGTCATGATGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000029252:ENSDART00000041627:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF142591=RRM_6=FE(51.5=100)
A:
NA
C2:
PF142591=RRM_6=PD(41.2=80.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTTTCCTCTTGAAACTACGCT
R:
CGATCATCTCGTTTCCTTTGAAA
Band lengths:
199-2004
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]