Special

MmuINT0141281 @ mm10

Intron Retention

Gene
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:MGI Symbol;Acc:MGI:2387661]
Coordinates
chr2:124658410-124658819:+
Coord C1 exon
chr2:124658410-124658565
Coord A exon
chr2:124658566-124658645
Coord C2 exon
chr2:124658646-124658819
Length
80 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CCGCCTCTTTCCCCCACTAGGTA
3' ss Score
11.09
Exon sequences
Seq C1 exon
GCCTGGCTGTTGTGCCAAACACGGCCTCGCAGAAGCTTACAAGACCTCCATCGACTTTCCAGATGACACCCTGGCTTTCATCAAGTCCCACCCGCTGATGGACTCTGCCGTCCCACCCATTGCCGATGAGCCCTGGTTCACAAAGACACGGGTCAG
Seq A exon
GTGAGACCACAGGTCGTCTACTCCTACCCTTCTCTCCTGTCACAGGCCTCCTGATCTGACCCGCCTCTTTCCCCCACTAG
Seq C2 exon
GTACAGGTTGACAGCCATCGAAGTGGACCGTTCAGCAGGGCCATACCAAAACTACACAGTCATCTTTGTTGGCTCTGAAGCTGGCGTGGTACTTAAAGTTTTGGCAAAGACCAGTCCTTTCTCTCTGAATGACAGTGTATTACTCGAAGAGATTGAAGCTTATAACCCAGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027200:ENSMUST00000103241:16
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:
PF0140314=Sema=FE(12.2=100)
A:
NA
C2:
PF0140314=Sema=FE(13.6=100)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTCGCAGAAGCTTACAAGA
R:
CTGAACGGTCCACTTCGATGG
Band lengths:
168-248
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Pre-implantation embryo development
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types