Special

HsaINT0083902 @ hg19

Intron Retention

Gene
Description
junction plakoglobin [Source:HGNC Symbol;Acc:6207]
Coordinates
chr17:39914651-39915122:-
Coord C1 exon
chr17:39914967-39915122
Coord A exon
chr17:39914771-39914966
Coord C2 exon
chr17:39914651-39914770
Length
196 bp
Sequences
Splice sites
5' ss Seq
ACGGTATGT
5' ss Score
9.94
3' ss Seq
CCCTGCCTCCTCTCACACAGGAT
3' ss Score
9.35
Exon sequences
Seq C1 exon
GCAACCATCGGCTTGATCAGGAATCTGGCCCTGTGCCCAGCCAACCATGCCCCGCTGCAGGAGGCAGCGGTCATCCCCCGCCTCGTCCAACTGCTGGTGAAGGCCCACCAGGATGCCCAGCGCCACGTAGCTGCAGGCACACAGCAGCCCTACACG
Seq A exon
GTATGTGAGCTGGTGGTGCCTCTGACAGCCTTCCTGGGGGGTCAGGGTGTCCTCTGTGGGTGTGTGTGTGAATGGGGAGGTCAGTTGCAACTGATGCCAATTCCAAGAACCTGTGAAGTTCATTCGGCTGTCATGGGGAGGAGTTGTGGCCATGTCCAAGGCACCTGTCCCATGCCCCCTGCCTCCTCTCACACAG
Seq C2 exon
GATGGTGTGAGGATGGAGGAGATTGTGGAGGGCTGCACCGGAGCACTGCACATCCTCGCCCGGGACCCCATGAACCGCATGGAGATCTTCCGGCTCAACACCATTCCCCTGTTTGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000173801-JUP:NM_002230:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.135 A=NA C2=0.000
Domain overlap (PFAM):

C1:
PF0051418=Arm=WD(100=67.3)
A:
NA
C2:
PF0051418=Arm=PU(43.9=45.0)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTGATCAGGAATCTGGCCC
R:
TGTTGAGCCGGAAGATCTCCA
Band lengths:
246-442
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Autistic and control brains
  • Pre-implantation embryo development