DreINT0095822 @ danRer10
Intron Retention
Gene
ENSDARG00000075963 | mhc1uba
Description
major histocompatibility complex class I UBA [Source:ZFIN;Acc:ZDB-GENE-990415-145]
Coordinates
chr19:7178393-7180272:+
Coord C1 exon
chr19:7178393-7178668
Coord A exon
chr19:7178669-7179978
Coord C2 exon
chr19:7179979-7180272
Length
1310 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
AGCCTGTCTCTCTCTCTCAGTCT
3' ss Score
8.95
Exon sequences
Seq C1 exon
GTGTTCACACCTTCCAGTTCATGTACGGCTGTGAGATGGATGATGATGGCAACAAACAAGTACATTGGCAGATTGGCTATGATGGAGAGGACTTCATCAGTTTGGATAAAAAAACGCTCACCTGGACTGCTGCTAATTCTCAAGCTATGACTACCAAGGTTAAATGGGATTCCACTGGAGCAGAGGCAAATTACTGGAAAGGATATCTGGAGAATGAATGCATTGAGTGGGTGCAGAAGTATGTGGGCTATGGGAAGGACACTTTGGAGAGAAAAG
Seq A exon
GTATGAATATTATTCGCTTTTATTGACCACTAGATAGTAAGCACTCATCATAACATTATCTACCTTTTAAGCTGGAAACTAAAAAGTTTCTTTAAGGTTTTGAAAATATGCATCTTTAATTTCTTCCTGCAGTATTAATTTTCTTGTTAATGATATTAATATGAAAACACTATGTAGTCTTTTACCCAAAAAAAATTTTTATATGTTATAAAACAACTTATTTCTGTTCATGCTATTTTCTATACAGTACATCATCTGATCTAAGTCTACATCAAAAAAACAGCTACTAGTTAGAACTAAAGTGAAAATTCCTCTGCAGTATATATTACCACACAATAACACAGCAGATTAGCAAATTGAATGATCTTCCTATCACTATATTAGAATAGTCTAAAAGAAAGAGACTGTACTGTATATGAAACATGAAATCAAGGGATAAGATTCATAATTACATGTTTTTGATTGTGTGATAAGTCTACTGATGTGTACTGTACTTGAAACTACAATAGATAGTCAGAAGAAATATTTAGCAATTATTTAATTTGAGTTTGAAGGCTCTAATTTTGCCTGTCTCAGTTCATTACCTTAGTCATCTCTCTTTAATATTTGCTTTATTGGCATGAAAAATTTTACAAATGTATTGGCAAAGCAGTTATAAAGTTTACATAAAAATAAAAGAACATACATATACAATAAAAACACAGTAAACAGTAGTAGTAGTAGTTGTAAAAATATAAAAAAGATATCTACATGTAATAATTAAATAAAAAATATAAATAATATATCATTATTCAATATATCATATTATAATTCAATATATTATATCATTCATATCATATTATTTATTTATAACAATAAAGGTAATAATAGATCAGAATAAACTGTACATTTAACAATCAACATTTTAGGATGACAGTAATAAAAACAATAATAATCTGTATATTTACAATTATTTAATTAGAATTATCTAGGTGTGTGTGTGTTTGTGTGTGTTTGCAAGCACATCACTGATGTTTTTATTGGTCTGCTTTCTCTTTTTGTGACAGGCATTAATGTATTTGGCCGCTAGAAGGACAGAGTCTGTTTTTTCTCCTAGTAAATACTGAAGCTGTGTTTTATTGTCTAACTCAGTGAATTGTGGGTAAATGCTCTGTAGTTTGGGGTAGATTGTTTCTCTCATGTGCTGATATAATGTGCAGCAGGTGAGGAAGTGTTCCTCCATCTTCACCTCTGCTTGGGCACAGCGTGGGCAGATGCGGCTCTCTCTGGGTTGCCAGTTCTGTCTGTATCAGCCTGTCTCTCTCTCTCAG
Seq C2 exon
TCTCTCCTCAGGTGTCTCTGCTGCAGAAATCTTCTTCTTCTCCAGTCGTGTGTCATGTTACAGGCTTTTACCCCAGTGGTTTAAAGATCTCCTGGCAGAGAAACGGACAAGATCATGATGAGGATGTGGAGCTTGGTGAACTTATCCCAAATGAGGACGGAACCTACCAGAGAACGAGCACTCTGAATGTTAAACCTGAAGAGTGGAAGAAGGACAAGTTCAGCTGTGTGGTGGAGCATCAGAGCAAAACTATCAACAGTATTCTCACTGAAGACGAAATCAGAACTAACAATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000075963:ENSDART00000009689:3
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=0.263
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(50.0=94.6)
A:
NA
C2:
PF0765410=C1-set=WD(100=87.9)
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:
CCACTGGAGCAGAGGCAAATT
R:
TTTGCTCTGATGCTCCACCAC
Band lengths:
353-1663
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]