Special

MmuINT0141119 @ 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
chr7:87368820-87371410:+
Coord C1 exon
chr7:87368820-87368902
Coord A exon
chr7:87368903-87369481
Coord C2 exon
chr7:87369482-87371410
Length
579 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CATGCCTATTCTGCCCACAGGTA
3' ss Score
11.94
Exon sequences
Seq C1 exon
GCCATGGACCCAGGACATTGAGGGTGCCAGTGTCAAGGAACTCTGCAAGAATTCCTCATACAAGGCCCGGTTTCTTGTGCCAG
Seq A exon
GTAAGATGCCCTGGGAAAGGTGAGCCATATTTGCTTGGAAAACACCTCTAGGTATTTTTAGGTACAAATTTATTCCTCTAGCCCTACAAAGAAGAGTCCAGATCATGAGTCACTTAGTCCCAACCATCGCCCAAGTTACCATTGGTCCTAGTTAGAGTTTCTGTGGCTGGGAAGAGACACCATGATCACAGCTCTTATAAAGGAAAATGTTTAATTGAGGTTAGCTTACAGTTCAGAGGTCAGTCCATTATTGTCATAGCAGGAAGCATGGTGGCATTGCAGGCAGACATGGTGCTGGAGAGGTAGTGAGAGTTCTAAATCTGGATCAGTGGACAGCAGGGAGAGAGAGTGTCACTGAACCTGGCTTGGGCATCTGAAACCTCAAGGCCCAGCCCCAGTGACACACTTCTTTCAGCAAGGCCACACGTCCCAATAGTGTAATTAATTGCCTTTGAGCCTATGGGGCCATTTTCATTCAAACTACCACACTATCATAGCACCAGATTGAGGAGGGTGGGCCTAAGTCTGGAGCTGCTCTGGGCAATGACCTCTTCTACCCCATGCCTATTCTGCCCACAG
Seq C2 exon
GTAAGCCATGTAAACAAGTCCAGATCCAACCAAACACAGTGAACACCCTGGCCTGCCCACTCCTCTCAAACCTGGCCACTCGGCTCTGGGTGCACAATGGAGCCCCAGTCAATGCCTCTGCCTCCTGCCGCGTGTTACCCACCGGGGACCTGCTGCTGGTGGGCAGCCAGCAGGGTTTGGGGGTGTTCCAGTGTTGGTCGATAGAAGAAGGATTCCAGCAGCTTGTGGCCAGCTACTGCCCAGAGGTGATGGAGGAGGGGGTAATGGACCAAAAGAACCAGCGTGATGGTACCCCAGTCATTATCAACACATCACGAGTGAGTGCACCGGCTGGTGGCAGGGCCAGCTGGGGTGCGGACAAGTCCTACTGGAATGAATTCCTGGTGATGTGTACTCTGTTTGTGTTTGCTATGGTGCTTTTGTTTCTGTTCTTTCTCTACCGACATCGGGATGGCATGAAACTCTTCCTAAAGCAGGGCGAATGTGCCAGTGTGCACCCCAAGACTCGCCCTATAGTGCTACCACCTGAGACCCGACCGCTGAATGGTGTCGGCCCTCCTAGCACCCCACTTGACCACCGAGGCTACCAGGCTCTGTCGGATAGCTCCCCAGGGCCCAGAGTCTTCACTGAATCAGAGAAGAGGCCACTGAGCATCCAGGACAGCTTTGTAGAGGTGTCTCCCGTGTGTCCCCGGCCCCGAGTTCGACTGGGCTCTGAGATCCGAGACTCTGTGGTATGAGAGCTGACTTTAGATGTGGTCACCCTGACCTCAGGGGTTGTGAGTGTTCAGTGGAGGTCAGCTACCTCTGCTTCTCACAGAACACAGCCACGGTACCCTGACTGGAGGGCAGCTGGTACCACAGGCCCAACAGCCCAGCCAGCTGCTTCCAGTGTCTGGCCGAGAACTGGGCTGCCTCCAGGGGCCAGAGGGTCCTTGTCTGGGTGGCAGAACTCTGCTACTTAACTGAGCCCTTTGTTTAAAACTGCAAATGTGAAGCCAGAGAGGAAGGAGAAACAGACAAGGAAGACTACAACATAGCCACTCCAGTTCAGCCTGCTGGGCTCTTGGGGACTTCTCCAAAGTGGCTTTGTGAGCAAGCCGAAGTTGAGAATCCCTCCCCGACTGGACTATTCTACCTTCCGCCTTACTCTGCTGCTGAGGCTACCCTTTCTCACTGCAGAATCAGGGCCCTGCTCCAGCTTCAGCCAACCGAGGACATATCTGTGACCGCTGACACCCTACCACCTCAGGGACCAGAGGGCTAGGCTGATTCTGCAGCCCTCCTCACCAGACCCTGGGCTCAGTCCCAGTTCCCGGACTTCTCCAGCCTGTATCAGGCTGTGGCCTCAAAAGCAAGGGAGTGACCCCCAAGGGGGGTTGTGACAGAAGACTTGCCTACTGTCCTTTTCCCAGTCAGAGAACTATGTCCCTACCCATCGACGTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTTCGAGACAGGCTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGTCTCGAACTTAGAAATCCGCCTGACTGCCTCCCAAGTGCTGGGATTAAAGGCGTGTGCCACCACTGCCCGGCCCCACCCATCTTCTAATTCCTACACAGACTCCTGGATCCTCGTTCCTTGTCCTAGCTCACCGTGCCCGTCACTCTAAGGGATGCTGACACTGCCCATCACAAGGACCCTGAATTTACATGGGTTTTATATTTTTTTTTAATAAGATGCACTTTACTTTCTTTTTTAAATAAAATCCGACAAATTATAGTTATTTGTGGCCCACATTCCTGAAGGGCTTTGCTTTGTGTGTATGTGATATGAATATATGTATATGCGGAGACCAGAGGCTCTCCTTTGCTTTGTGTGTATGTGATAGGAATATATGTATATGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030539-Sema4b:NM_013659:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.154
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0143720=PSI=PD(32.8=65.5)

							
A:
NA

							
C2:
PF061436=Baculo_11_kDa=WD(100=15.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000032754





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr15:90227643-90227903 
LOW PSI
HsaINT0147338
(SEMA4B)
Human
(hg19)
chr15:90770875-90771135 
LOW PSI
HsaINT0147338
(SEMA4B)
Rat
(rn6)
chr1:142012175-142012701 
LOW PSI
RnoINT0132929
(Sema4b)
Cow
(bosTau6)
chr21:22040307-22040580 
LOW PSI
BtaINT0130809
(SEMA4B)
Chicken
(galGal4)
chr10:19534646-19534725 
LOW PSI
GgaINT0028629
(SEMA4B)
Chicken
(galGal3)
chr10:22201607-22201686 
LOW PSI
GgaINT0028629
([1])
Zebrafish
(danRer10)
chr18:25797681-25797946 
LOW PSI
DreINT0132707
(sema4ba)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CCTCATACAAGGCCCGGTTTC

				
R: 
GTGCACTCACTCGTGATGTGT

				
Band lengths: 
357-936

			

		

	





	
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"