Special

MmuINT0141118 @ mm9

Intron Retention

Gene
ENSMUSG00000030539 | Sema4b
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B [Source:MGI Symbol;Acc:MGI:107559]
Coordinates
chr7:87365674-87368902:+
Coord C1 exon
chr7:87365674-87365840
Coord A exon
chr7:87365841-87368819
Coord C2 exon
chr7:87368820-87368902
Length
2979 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CAAGACTCTTTTATACCCAGGCC
3' ss Score
4.39
Exon sequences
Seq C1 exon
GGACTGTTGTATGCCTCCTCCCATTCCGGGGTGGTGCAAGTGCCCGTAGCCAACTGCAGCCTGTACCCAACCTGTGGAGACTGCCTCCTGGCTCGAGACCCCTACTGCGCCTGGACTGGCTCTGCCTGCAGGCTCGCTAGCCTCTACCAGCCTGATCTGGCCTCCAG
Seq A exon
GTGAGAACTCCCAAAGACCCAGTGACTCCTCCTCATCTCTGAGCACTGCATCTTCTCTGGGACCCCTGCACATGGTTATTTCTCAGCTCTCTGTGGCCATATAATCTATATGGACCAGATAGACAGGGTTTGCCAGAATAAGAAACATCTAGTAAAGAAGATGTGGATTGCCACATGCACATAGCTTATTGTAAGTAGGCTGTTCGGTAAGCCTGTTAGACCATTAAAAAGTAGAGTAACATTAGAATTAGAGATGTCTATTGAGAAAACAGAGATGTGCTATTTGGCACAGTGATGCACAGCTTTAATCCTAGCATGCAGGAAGCAGAAGCAGGAAGATCTTTGTGAATTTAAGACCAGCCAGGACCACATAATGAGACCCCGTCTCCATTTAAATGAAAATAGGAATGAGTCAGCTGAAGTGGGGTTTGTCTGTAATCCAGTGCCTGGTTTTATTGTTGTTCTGTTGTTTGTTTTTGGTTTTATTGAGGCAGGGTCTCATGTAGCCTAGGATATAGTGGTGGATGCTTAGAAGAAGATGGGGTGGCCAGGACCTGCTGGTGCATGCGTATAATCCTACTGTTCAGAAGGTGGAGGCAGGAGGGTCAGAAGTTCAAGGACATCCTCTGCAACAAAGAGTTTCAAGGCCAGCAGGAGTTACAGGAGACTTTGTCTCACAAAAATGGATGGTGCTGGAGACGTGGCTCAGCAGTTAAGAGCACGGACTGCTCTCATAGAGGACCCAGGTTTCATTCCTAAGCTCCCATATCAGGCAGTTTACAACCAACTGCTTAGAACTGGCTTCCTGCATACACCTGGTACAGGAAATTCACCTAGGTATAGGCAGATGCACATACGTAAAAGGAATACGTAAATATTTAAAAAAAAAAAAAAAAAAAGACGAGAAGAGGGATGTTCTCCAAGTGAAGCTCTTCAGCCCTATCTGTGGACTGGATTTTAACATGGCTTTGTATTTCCCTAAAATGGGTCAAACGAATGATCTCATTGTTTTATTACAAATGGGATCTCTCATTTGTAGTTTTCTTTTGTTTATATCAAAAGGACACAAATTACTGCACGCTTAAAGCACAGAAGTCATACACTCCCTTAGCCGTATCCTTGTCTTATAGGTGGTATGGCTGGTGTCTATCTTTAAACTTTTTCAGGAACTTCCATATTTGGGGATGATTTTGTGTGTGTGGCCTGAAGTCCCGTTACTAGGGGGGTGGAGGCAGGACGATCTGTAGTTCAGAGTTATCCTTGACTACATAAAAAGTTTAGGGCTAGCCTAGGCTATATAACTAAGACCCAGTTTGGGCTAGATGCTCTGGCAAATGCCTTTAATCCCAGGGTTCAGCAGGCAGAGGCAGATAGATGGATCTCTGTGAGTTTTGAGGCCAGCCTGGTTTACACATTCATTGAGTTGCAAGATAGTCAGGGCTGTGCAGGAAAAAAAAACAAACAAACAAACAAACAAAAAATCCCTGTTTCAACCTCCCTTTCCTCCCCCAACTCTTGCACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACCCAGTAAAACAAAACAACAGCAGCAGAAACCCTGATAAACTCCTGGAAGCATGGATGTAAGGTCTCCCTTGGCTGATTCATAGCAGATTCTGGGCAACTTCTGTAGTGCTTGTATTCTTTATGCTTGGTTGAGTTTTATTTTCTCCTTTTTTGAGACAGGGTCTCACTATAGCCCTGGCTAGCCAGGAATTCACTATGTAGACCAGGCTGGCCTCAAACTCACAGAAATCTGTCTCAGCTTCCCCAAGTGCTGGCATTAAAGATGTGTACTACACTGCCTGGCTGAGCTTTCTAACTTATAAGTGCATGAAAATTCACCTTTTCTAGTTACACACCTGTAACCCCAAAACTAGAGAGTCTAAAGTAAAAGAGTTTGCAGTTGGAGGGAGGGTAGCCTGGGCTACCTTGCCTATCCTAGCCAAAAAAAAAAAAAAAAAAAGAATAAAAGGAAAGCCTGGCTTGCTTTCCTTCCTCCTTCCTTCCTTCCTTCCTCCTTCCTTCTTTACTTCCTTCCTTCCTTCCCTTCCCTCTTTCTTCCCTTCCTTTCCCTCTCTTTCTCTCCCTCCCTCCCTCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTTCTTCCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCGACAGGGTCCTGCTCTGTAGCTAGGACTGTTGTGCACCTCATGGCCATTTCTTGGGTTTTTAATTGCCTTCTTTTGTGGGAGGGTAGTATTTCAGACAGGGTCTCATGTAGCCTAGACTGACCTCCAGTTCACTGTGTTGTGAAGATAACTTTGGATTTCTGTACCTCCTGTGACTACCTCCCAAGTGCTAGGCACATTCTGCTTTTATAGCAAAAGGGGGTTGTTTGTGACTTTATTTGTGGTAATGTGTAGACGGGGTCTGAGGAGACGGCTCAGACCGTGGAGTACTTGCCTCAAAAGCGTGACAATCTGAGTTTGATTCTCAGAACACACATAAAAATGCCGAGCATGATGGTGGCAAGAAGTACCCCTGTAGTTCCCTGCCCATCTGATCTTTCCTAGTTGTTAAACTCCAAGCTAATGAGACGCTGTGTCTCAAAGGAGGTGGATGGTGTTCATAAGGATGACACCAAGGCTGTCTTCTAAACACACACACCTGTAATTATGACTAGAAATACCCAGTCAGCCCCATGGTGGTGGGGACTCTGCTCAGGCAAGTCTCCTGCACCTGCTTTGGGCCTGGTGGGCTTACACCAGCAGTGGAGGGAAAAAGGAACACTGGCCAATGGGATTCTACCCAAGACTCTTTTATACCCAG
Seq C2 exon
GCCATGGACCCAGGACATTGAGGGTGCCAGTGTCAAGGAACTCTGCAAGAATTCCTCATACAAGGCCCGGTTTCTTGTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030539-Sema4b:NM_013659:13
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:
PF0143720=PSI=PU(65.5=67.9)

							
A:
NA

							
C2:
PF0143720=PSI=PD(32.8=65.5)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000103006





     
                   









    
Main Skipping Isoform:
ENSMUSP00000032754





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr15:90225828-90227556 
ALTERNATIVE
HsaINT0147337
(SEMA4B)
Human
(hg19)
chr15:90769060-90770788 
ALTERNATIVE
HsaINT0147337
(SEMA4B)
Rat
(rn6)
chr1:142008989-142012091 
ALTERNATIVE
RnoINT0132928
(Sema4b)
Cow
(bosTau6)
chr21:22038313-22040226 
ALTERNATIVE
BtaINT0130808
(SEMA4B)
Chicken
(galGal4)
chr10:19534461-19534550 
LOW PSI
GgaINT0028628
(SEMA4B)
Chicken
(galGal3)
chr10:22201422-22201511 
LOW PSI
GgaINT0028628
([1])
Zebrafish
(danRer10)
chr19:24800605-24800759 
LOW PSI
DreINT0132692
(sema4ab)
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"