Special

MmuINT0036309 @ mm9

Intron Retention

Gene
Description
cholinergic receptor, nicotinic, gamma polypeptide [Source:MGI Symbol;Acc:MGI:87895]
Coordinates
chr1:89104783-89105790:+
Coord C1 exon
chr1:89104783-89104880
Coord A exon
chr1:89104881-89105589
Coord C2 exon
chr1:89105590-89105790
Length
709 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACC
5' ss Score
8.66
3' ss Seq
TAGTAAAGTTCTCCCCACAGAGA
3' ss Score
5.32
Exon sequences
Seq C1 exon
ATCCCAGACTTACAGCACCAGTGAGATCAACTTGCAGCTGAGCCAGGAGGATGGGCAAGCCATTGAGTGGATCTTCATTGACCCGGAGGCTTTCACAG
Seq A exon
GTAACCCCAGCTAGGAGCCCCTGCCCGGATTGAGGCTATGCCCCAACCCCAATACTCTTCAAGGTGAAAACTACAGTGTATCCTGGAATATGGCTTTCAAAAGGTCTCAACAGAAGTCCAGACATGGTGACACACATACATGATCCCAGCCCCCCTGGAGGATTGAAAGTTTGAGGCTAGCCTGGCTACACAATGAGACTGTCTTTAAAGAAAAACGCAGGAGGGCTGGGAAGATGGCTCCATGGGGGTAAAAGCACTTACTGCACATATGTGAAGACCAGAATTGAATGCCCAGAATTCACATAAATGCTGTTAGAAATGGGAGCCTACCTGAAATTCCAGCACAAGTCAGATAGAGACAAAGGATTTCTAGGGCAAAGCTCTGGGTCCAAGCGACAGACCCTGCCTTGGCATAAAAGGTGAAGAGTGTCTGAGGAAGACACCTGATGCTGAATTCTGGCTTCCACGTCTGTACACACACACACACACACACACACACACACACACACATGCACACACATACATGTGAGTATATGCATACATGTGTGTATATGCATACACACGCATGCACACATACACACCGAAAAGGATCCAGGGAAGTTCTGACTCTTCCTATGATACTTACTCTAGTTTTGGGAGGGGAGATCAATATTCAATCTCCCACCCCACTTGTGTCACTTTGTGATGCTTAGTAAAGTTCTCCCCACAG
Seq C2 exon
AGAATGGGGAGTGGGCCATCCGGCACCGACCGGCTAAAATGCTCCTGGACTCCGTGGCTCCTGCAGAGGAGGCGGGCCACCAGAAGGTGGTGTTCTACCTGCTTATCCAGCGCAAGCCCCTCTTCTACGTCATCAACATCATCGCCCCCTGTGTGCTCATCTCCTCAGTCGCCATCCTCATCTACTTCCTTCCTGCTAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026253-Chrng:NM_009604:6
Average complexity
IR-C
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:
PF0293118=Neur_chan_LBD=PD(3.2=8.8),PF0293118=Neur_chan_LBD=PU(45.2=97.1)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(18.1=57.4),PF0293211=Neur_chan_memb=PU(8.5=30.9)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
ALTERNATIVE
Zebrafish
(danRer10)
LOW PSI
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCCAGACTTACAGCACCAGT
R:
AGCAGGAAGGAAGTAGATGAGGA
Band lengths:
294-1003
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

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