Special

MmuINT0139211 @ mm10

Intron Retention

Gene
Description
secretory carrier membrane protein 5 [Source:MGI Symbol;Acc:MGI:1928948]
Coordinates
chr9:57446072-57447233:-
Coord C1 exon
chr9:57447077-57447233
Coord A exon
chr9:57446174-57447076
Coord C2 exon
chr9:57446072-57446173
Length
903 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
AACCATCTTCTCTGCCATAGGAC
3' ss Score
9.46
Exon sequences
Seq C1 exon
TGAACAGCGTCACGCTGGCCGTGAACCTGGTGGGCTGTCTCGCGTGGCTGATCGGAGGCGGGGGAGCCACCAACTTTGGCCTGGCCTTTCTCTGGCTCATCCTCTTCACACCTTGCTCCTACGTCTGCTGGTTTCGGCCCATTTACAAGGCCTTCAA
Seq A exon
GTAAGTGGTTGGTGCCGACCCCAGCTCCTACCCCTATTTCCCTCTGACTGCTGTTCCACACTCTTATCTTCTGTTTCCCTTGGGATTCCTGGGAGTTCCTGGCTGGGTTGAGAGGGTTGGGAGTGGGACCTTCCTTAGTTCCTTCCTTCTTCAGTTTTCCCTTCTTGTTAAGTTTTGCCTATGGGGCTGTCTTGGTGGAGCTGTCCATCCTTGTACCAGTGGGGAATGACTGGTTTGGTACCAAGAAAACCCTTTATTCACGTGTCAGTGGAAGTGGCCATCTAAGACCCATGGATGCTATTCATGGGCCAATGATGCCATCCAAGCCTGTGCCAAAGGGAATACCTATCTATGTATTGATGGGGTGCCAGGGAGTGTCTATCCAGTGCCAACTGGGATTTCCATTTTTTGTGCCATTAGAGCTGCAAGACAGCAACAAAGCTGTCTTGGTGCCAGCAGAATATACATTTCAGTGCCATGGAGCCTTAAATCTCTTTATCGACAGGACTCACCATCTATGTGCCAATTAGCTACTGTTTGGTGTCAGTAAGGTCTCTTTTCTATGCCACCGAGACTTGCTGTTTCTGAGTCTATAGAGCCACCCACCCCCATTCCAGTTCCTTGATAATGGAGCTGCTTGCTTTTCCCACAACAGAGCCAAGTATCGCTATGCCAGTAGGGCCGTTAATCTATGTGCTACGGATGGACGGTCCTTTTATGGGGGCAGCCCTTTCTTGCACACAGGCCTAGCTCATCTCTGAATGAAGGCCATCCTTTTTACATTCTCATTCAAAGCACACTTGTGTTGTTTGCTCGTCCTTTTGCCCAGAGGAGCTTTGGGAGCTCGAGTGCAGGGAAGCCCAGTGCCTCTGCCCAGGTGACAAACCATCTTCTCTGCCATAG
Seq C2 exon
GACAGACAGTTCCTTCAGCTTCATGGCATTCTTCTTCACCTTCATGGCTCAGCTGGTCATCAGCATCATCCAGGCTGTGGGAATTCCAGGCTGGGGTGTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040722:ENSMUST00000046587:4
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:
PF041448=SCAMP=FE(29.4=100)
A:
NA
C2:
PF041448=SCAMP=FE(19.2=100)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
ALTERNATIVE
Chicken
(galGal3)
ALTERNATIVE
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGGCCGTGAACCTGGT
R:
CAGACACCCCAGCCTGGAATT
Band lengths:
246-1149
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