Special

MmuINT0141261 @ mm9

Intron Retention

Gene
ENSMUSG00000038777 | Sema6c
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:MGI Symbol;Acc:MGI:1338032]
Coordinates
chr3:94968296-94971042:+
Coord C1 exon
chr3:94968296-94968435
Coord A exon
chr3:94968436-94970927
Coord C2 exon
chr3:94970928-94971042
Length
2492 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TATACCACCGTACCCTCCAGGTG
3' ss Score
8.03
Exon sequences
Seq C1 exon
GTGAGCTGCCCCGCACAGGATGCCCCGTGCCCCCCACTCCATGCCCCTGCTGCTCCTGCTGCTGTTGCTGTCATCGCTCCCCCAAGCCCAGGCTGCCTTTCCCCAGGACCCCACCCCTCTGTTGACCTCTGACCTTCAAG
Seq A exon
GTGAGTGCTCCACCCACTTTGCCCACTTGGGGGGGGGGGGTGCAAGTAGAGAATGAGAGAGAGGCAAGGAGTGAGGATGTTCCCAGTCTTAGGGAAGCTAAGAGAATGGCCAAGCAAAGGGGAACAAACAGGTGGGATGAGCTGGAACCTCACGCTTCTCATCCCTGGGCATTTCTTCACTCAGAGGTAGTGTTGCTAGGCGGCTAAAGATGTGACCTCTAGCTGAACGTGATGGTTGCATGCTCACAATCCCAGCACTTGGGAGTCTGAGGGAGGAAGACTGCTACAACTCTGAAGACAGCTTGAGCTCTGTAGTGAGTTCCAGGCCAGTTGGCATAACATAGCAAGAGCCTGTCTCAATAGACAGACATAAGGAGTGCAAGGTCTTAGCCACACCAAACCACGGCAGGTATGAAACCCTGCTCATCTGCTCGCTAGATTCGTGTTATCTAACCTTTCTTAGCCTCAGTTTCCACATCAATAAAAGGAAGATAACCATAGTGTTATATCTCGTGGTGTTACTCAGAGATTAAGTGAGGTGACAGATGTAACGCAAATGAGGCACAGTCCTGAGAACACTGTCTGGTCCAGATTAAGCACTTTATGTTTGTGTGTTATTCTTAGCTACAAAGTGGAGTCCTGTGCCAGGCCAGTGGTTCCCAAAACCCTTACTTCTCCTCTGCCTACCAGAGAGCCTAGGTCTCACTATGACAGAAACCATAAATCTACCCTTTCAGAGAAAAATCCTTCACCTGTGCTCTAGATGTTGGATTTATATTTATTTCAGTTGGGCTACTAGGGGTGACTGTTGGGGGACAGATAAGACTAGCAAATACTACATCTGACGCAGATCCCAGCACTCTCTCTGTTAAATCATCTGTGAACCCTGGGTTCCCTCATCAACACCAATACCTGAAGCTTTTATGCCCAGAACAGGTAGACAATGGAGTTGGTCACAATGGCGAAGTGTTGAAAGTCTTGAGGGGGATTCGAAGAGGGGTAGGAGAAGCAGGTGCTTTAATTATGTATGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAGGAGCTGTTGTATGACAAAACTTTTCCTGGGGAGATGGAACACGTCTACTGAACCCAGATAGGGAGGCCAAATATGGATACCACCAAAGTCAAACTTGGTGAACTGAGAAGTTTTACTGGGGGTACTTACAGAAATATGGGTGAGGGGTTACTTACAGGAGCAGAAATGACTCAGAGACAGCTGTACCACCAAAGCCCACTCCAGTATGGGCACTAGCTTGTAAGCTGGAATTGGGAGCACAGTACACAGCCTGCAGGCAGCTCACCTATTGGAGAGTCCTTTTCAGGTATCTCAGTTGGCCTCTTCCAGGCAGTCTCTTCTCTGCAGCTCAGCTTCATGTCCTCTGAGGGGGACCCTAGCTTTTATTAACTCTGACAGGGAAAGGGCCAACTGAATCTGGTCAGTTTCAGGGAGTTCTTGAAGCTGTTTTGTTATTTACCTCCCTGCGTATGGAGCTGGCCAGCAGAATGGATGTTTTAATCTCAAGGAGAACAGAGGAGGTAGGTTGCTTGGAGTTGGAGCTAGAGGTGGTTGTGAGCCACCTGATGTGGGAGCTGGGAATCAAACTCTGGCCCTGGAAGCGCAGTGCATGCCCTTAATCACTAAGCCATCTCCAGCCCCTTGAAAGGAACTTTCTAACACAAAGGTGGTCGGTCCTAAGAAGGAACTTGGCTCAACTCTGGAGCAGGCCCTGCCGCCTACATGGCAGTCATGTAAATCCCTCAGTGCACTAAGCCTTGCAATGGGGCCAAGGTGAACTCCCACCTATAAGGTTATGAAGGAAGGTAAGTCATTCAAATGACTCACAGTATCTGATGAAAGTGAAATGCTGTTATGGTGTTTTTGTTGTTGTTTGTTTAACAGTTTTTATTTGGGGGGAGTGTACATGCCATAGTGGATGAGTGAAGACTAAAAGGCAACTTGGGAATTGGTTCTCTGCCTCCACTATGTGAACTTTGTAATCAGGCTTGGCTGCAAGTATCCAAGTATCTCTAACCTCAGAGCCATTTCAACATCCTGTTTCTTTTTTTTGTTTTTGTTTTTGAGACAGGGTTTCTCTGTATAGCCCTGACTGTCCTGGAACTCACTTTGTAGACTAGGCTGGCCTCAAACTCAGAATCCGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGTGTGCGCCACCACGCCCGGCCTCTTCCTTTTGACATAGCATCTTGCCTTGTACTTGCTATGTAACCAAGTCTGGCCTTAAACTCTTGGCAGTCCTCCTGCCTCAGCCTCCCCTAGTGCTGGTGTGCAACACTATGCCTAGCTTCGGGTACTGTTTTTAGTAGTAGGTTTTGGGCCTCTCTTCGTGGCTGAGTTCCATCTGGTAGGAAGTACGTATCATCTCAGCTGCCATGCTCAGTATACCACCGTACCCTCCAG
Seq C2 exon
GTGCCTCTCCATCATCCTGGTTCCGGGGCCTGGAGGACGATGCTGTGGCTGCGGAACTTGGGCTGGACTTTCAGAGATTCCTGACCTTGAACCGGACCTTGCTTGTGGCTGCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038777-Sema6c:NM_011351:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.098 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0140314=Sema=PU(11.0=35.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000072590





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000088331, ENSMUSP00000088333, ENSMUSP00000102835, ENSMUSP00000123457, ENSMUSP00000129081
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:151140091-151142503 
ALTERNATIVE
HsaINT0147497
(SEMA6C)
Human
(hg19)
chr1:151112567-151114979 
ALTERNATIVE
HsaINT0147497
(SEMA6C)
Rat
(rn6)
chr2:196334780-196337390 
ALTERNATIVE
RnoINT0133072
(Sema6c)
Cow
(bosTau6)
chr3:19719652-19721266 
LOW PSI
BtaINT0130952
(SEMA6C)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr28:2063765-2063915 
GgaINT0144564
(SEMA6B)
Zebrafish
(danRer10)
chr19:406711-407606 
LOW PSI
DreINT0132862
(sema6d)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
Functional annotations
(Submit an annotation)

	


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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"