HsaINT0052429 @ hg19
Intron Retention
Gene
ENSG00000046604 | DSG2
Description
desmoglein 2 [Source:HGNC Symbol;Acc:3049]
Coordinates
chr18:29121156-29122815:+
Coord C1 exon
chr18:29121156-29121277
Coord A exon
chr18:29121278-29122482
Coord C2 exon
chr18:29122483-29122815
Length
1205 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
AGCTGTGTTTGCTCTCACAGGTG
3' ss Score
10.37
Exon sequences
Seq C1 exon
TGGTACCACTTTTACTGCTGATGTGCCATTGCGGAAAGGGCGCCAAAGGCTTTACCCCCATACCTGGCACCATAGAGATGCTGCATCCTTGGAATAATGAAGGAGCACCACCTGAAGACAAG
Seq A exon
GTCAGTGGATCAGATGTCAATATGACTTGTCTTCTTCTTGGGTTTTAAAGGGGCCTAGGGAAGTGTTTCTTACATGTTTGGTTGAGTGAGTAAAGTGATCACTATGGATTTCACTCATGTGCCTTTGTTAAGCAAAGAGTTCAAATGACAGCATATTTTGTGTTTGTTGCTGGGGCAGAATTGAGATAGTTTTACTCTGTTTTGACACTTCCCATGTTGTAGAGAATGTAGAGCAAGGTTCAGGAAGAGCAAGAGTGTGTAGGAATCTAAGTCTTTTGTCCTAACATTAAATGGGCAGTTTTCATAACCAGGAACTGCTTCATTTCCATTTCCCTCAATACATAGGGTTTGCAGAGGTAAGCCCACAACCCCCATGACACTTGTAAAATGTTGCAAAACCCCATTTCCCAACTACATCATAGCCATATCCCTTTGTCTCTCTGTTGCACCTTCACCCTGGACCTCTCACCACCATCTGTTATGAGCACCATTTCTAATAGGATAGGATTTAGCATCAGGTGGCAGAGAACTCAGAATAACAGTGGCTTAATCCTAAAATGGGCATTCCAAGATCAACATGATGATTCATCCGCAGCATGGTCCCCAGTTCCCTCTTCCTTGTTTTTCTTCCATGGTTGAGTTCCATTCCCACACTGTCCTCATGTCCTAGTTCTAGCTACCTAGCTGCCGTCCCCACATTCTAACCAGCACATGGGAGAAAAGTGAAGAACCCTCTTTAAGCACACTTCCCGGAACTTGTGTACACCATTTCTGCTTCATTCACATTGACCACAGTTTAGTCAGGTGGCTATACCTAGTGGCATCAGAGGCTTAGAAATATAGTCTTTATTTTGGGTGGCCATGGATCCAGGTCAAAACAAAGTTAAGAATTCTGTAACTATAGAAGAAGGTATCAAACTGTAGAGGGAGGTTGAAATGCCATTGGTCGCATAGAGTAAAGGAGCTGAGACTGTTTGGGCTTTGTTTTCTCTTTGGGTTCTATCCACCTATAAAACAAGAAGAGAGAAGAAAGGAGATCTTCATAAGACTTACATAAGTTATTCAACTCAAAATACTTTTTCTAACTGGCCTCAGTGGAAATAGCTTATACCTTCCTATGCCCACTTGACTCAGATCCTTCTACCAAGGATGAAGGATTCCCTCCATCCTCCTGACTCAGTTCTCAGCTGTGTTTGCTCTCACAG
Seq C2 exon
GTGGTGCCATCATTTCTGCCAGTGGATCAAGGGGGCAGTCTAGTAGGAAGAAATGGAGTAGGAGGTATGGCCAAGGAAGCCACGATGAAAGGAAGTAGCTCTGCTTCCATTGTCAAAGGGCAACATGAGATGTCCGAGATGGATGGAAGGTGGGAAGAACACAGAAGCCTGCTTTCTGGTAGAGCTACCCAGTTTACAGGGGCCACAGGCGCTATCATGACCACTGAAACCACGAAGACCGCAAGGGCCACAGGGGCTTCCAGAGACATGGCCGGAGCTCAGGCAGCTGCTGTTGCACTGAACGAAGAATTCTTAAGAAATTATTTCACTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000046604-DSG2:NM_001943:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.317 A=NA C2=0.450
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0104912=Cadherin_C=PU(36.5=34.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGATGTGCCATTGCGGAAAG
R:
TTGCGGTCTTCGTGGTTTCAG
Band lengths:
349-1554
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
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)