Special

MmuINT0141177 @ mm9

Intron Retention

Gene
ENSMUSG00000025207 | Sema4g
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G [Source:MGI Symbol;Acc:MGI:1347047]
Coordinates
chr19:45067610-45071057:+
Coord C1 exon
chr19:45067610-45067672
Coord A exon
chr19:45067673-45070958
Coord C2 exon
chr19:45070959-45071057
Length
3286 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
CTGCCTCCCTCTGTCTGTAGACC
3' ss Score
11.69
Exon sequences
Seq C1 exon
ATCCACTGGGAGGCCTCCCCAGAGATGCAAAGCAAGTGTCATCAGAAAGGGAAAAACAACCAG
Seq A exon
GTATGTGATCTCCCTGTCCCCAGCTCTCCTTTCTTCCTCCTCAACCAGGGGTGACAGAGTTGGAGGGACACAGACGGAGTGGGACAGATGTGCATTCAAGTGCACAACTGCAATGAGTAGTATGAGTGGCTGGCCTTAGGGTAACCCTTGGACTCCAACTATCTGTGGTCGATAGCTTGGCCTGTCACAGAAACTTAATCCCTTTCCCGGGAGATCTCAAAGTATAATCATAACACTAAGTAACTGCTAATAAGCGACAACTAGACCTAGTTCTAAAATAATCTGATGACGCATTGTTATACCCATTTTACAGCTAGGAAAAATGAGACTTTGCCGGACCCCTAGTCTACCTGGTGTTCATGGAAAGACATTAGTCAAATATTAGTCCTTTCTAACTAAAAGGCAGAGTGTCTGGGTTGGGGGTGGGGATCATGTCTGGTTAGGTAACAACCATTTAGAGAGCTTTTTAGGTTTTTTTGTACTTACTTATTTACTTTGGAGTTTTTGGGACAGAGTCTTACTGTATATCCTTGGCTGGCCTACAACTCACTCTGTAGACCAGGCTGGCCTCCAACTCACAAGCGATTTGCCGGCCTGTGCCTTCTGAGTGCTGAATTAAAGGTGTGTAACACCGCTCCTGGCTTGGAGAGATTTTTAAGACTACACTTTGGAAAGAATGGCATGGCTCAGCATAGGCACACACATAGACACACAAAATAAATAGATATAAAACAAAAAAAAATACATATTCTAAGCTAGTTATAGTAGCATATGTCTGTAATTCCAGCCCTTGAGGATAAATATATGCATATGCATATGTATATGCATATGTATATGTATATGTATGGGGTGTGTGTGTGTGTGTGTGTATGAAACAAAAAGTACACATTCACACTGGACATGATGGTGGCATGTGCCTATGACCCCAGCAGTTGGGAGTTAGAGGCAAGAGGATTAGAAGTTCAAAGAAAGCCTTGTCCTCAAACAAGTTTGAGGCTAGCCTGGGCTATATCAGATTTTTGTCTCAAACTAAAAGCAGTATACATCCCAAGTTCCACCAATGTAGAAATTCTGATTCAACAAGTCTGTGGTATGTCCCTCTAAAATTTTCTAGGAGAGACTCCCTCAGTGCATTGTGGGTAATAAACAGAGCTAGTGGGACAGGTGAACCCAGGTCACAAGGTCTCATAAATGCCCAGTGGAGGGTTTAGACTTTATTGTGACAATGATACTCATACTGTTTGATGCCTTAGAGGCCCTCATGTGAATCACAGGTTGCGCATCAGTTGGTCTGAAAAGGCCCTAAGTTGCTTGCTGCCCTTGAAAGCCAACTAAAGCTGCTATCTCTGGTTCCCAGACCTCTTTAAGCAGCAAGGTATCAGAGAACATTTCCCAAAGCATTGTCCTGAAGGATACTCATTTTCAAAAGAGGGACTGAAGTGCTCTAATTTGTTTGGAAAGGGTTGACATTCCCATCCCACACAGTGACATCCTTAAGGCTCTGAGAAGTCACCCAGTAAAGACAGATGTGACTGCTTCTCAGGCTCGTTGACTACAGAATTCTTCCCAAACTGCCTTTTTTTCTGTCTCAGGGAGCTACTCAAGGAATGTCTGTCTCGCCCCACATTCACCCTGCATGCCAGATGAATTAAAATAGATGAGTCTAGAGGCAGGAAGAATGGTGGAATGGGGGCATCCTAGGGCTGAGGAAAAGGCCTGAGCAGGCTGATAAAAGGAACAGACATGGGTGACAGCAGGTGACGGCGTATAAGTGGAGAGAAGTCTTCCATGGACTCCAGCTCTGGGTAACAGACAAGAGGATGAGCAGAGAAAGCTGGACAGCAGCCTAGGGCACCTGAGGGACAGAGGAGGCCAGTGTGGCTGGAGTAGATGGAGTGAGCGGACAGGGAAGACAGGGGCATGTGGGCCTGTGTTGCCCTGTGTGGTCCAGTGTGTTCAGAGCATTGGTGAGCAGCGGCCATGCCATGGTCTGTTTTTACATCTGTGCTGCTGGGGCTGGAGAGATGGCTCAGCAGTTAAGAGCACTGACTGCTCTTCCAGAGATCCTGAGTTCAAATCCCAGCAGCCACATGGTGGCTCACAACCATCTGTAATGAGATCTGACACCCTCTTCTGGAGTGTCTGCAGACAGCTACAGTGTACTTACATATAACAAATAAATAAATAATTCTAAAAAAATACAAATTAAAAATTACATCTGTGGCTGCTTTGGAGAGTGGGTTGGACGGGCACAAGAGGGCACTGACAGATGGACCATCTCTGGAGGGAAACTTTGCACATGGTATCTACGATCCCCTTCTCAGGCCACCTGGGAGACAGGAATACATGACAGGCTGTTGACAACAGATCCCCTTGTCTGAATTTTACACTGTGAATACCTTTCACTCACAGAGTAAATGGTTGTTATGAAGAGTAGCATAGGTTAGGAGCATGTTGGGTGACTGCTAGGCCAAAGGAAGAGGTAATGGTTGTCTGGACCGGATGAGAATAGTGGTCTAGTTCAAGCACCACTTGGCCCAGTGACTCATGGAGCGGGACCGAATGTGGGGATGAGAGAGTGGGCTGCAGCCAAGATGCTCCTGAACCAGAGCAAGGTGGGGTGGGTGGAGCTGGAGGAGGGAAAGACTGGATAAACAGGTTTAAGAGGGATGATGTGGGCCAGGGGAAATGGAGCTTCCTTTAGGATAACGTGAGATTGATGTTGCTTGTGAGATAACAGAGAGGATTGTGGGAGCTCCAGGGTTGGGGGGGGGGGGGGACATTGCTCAGAAGTAACTTTTTTCCCGATGTTCACTCATGTTTGCCCTACGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTGGTGTGTGTGTGTGGTGTGTGTGTGTGGTGTGTGTGTGTGTGTTTGAGGATGTCATATCATAGAGTTACAGACAGTTGTGAGCTGCCATGTGGGTGCTGGGAATTGAGCCTGGGTCCTCTGGAAGAACAATGTTAACTGCTGAGCCATCTCTCCAGCCCCTCAGAAGTCACTTTTGAGCTCATGTCAAGCCCCCATTCTCCTGAAATGCTCCTCTATCTTTGAGCTCTGATGGTGCCTGAAAGTTAGGTGGAGGGGATAGCAGGAGACAGACACAGGAGTCACTGGAAGAGTGGTGTCAGGTAATCAGCGGCATCTTGGAAAGTATATCTGATAAGCTAGACTAATGGAGGTGGCTTGTCTCTGGGTTGATGAGTTCTATCACTGCCTCCCTCTGTCTGTAG
Seq C2 exon
ACCGAGTGTTTCAACCACGTGCGATTTCTACAGCGGCTCAATGCCACCCACTTCTATGCATGTGGGACCCACGCCTTCCAGCCCCTCTGTGCAGCTATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025207-Sema4g:NM_011976:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.571 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0140314=Sema=FE(4.6=100)

							
A:
NA

							
C2:
PF0140314=Sema=FE(7.4=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000026225





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr10:100973610-100977631 
LOW PSI
HsaINT0147401
(SEMA4G)
Human
(hg19)
chr10:102733367-102737388 
HsaINT0147401
(SEMA4G)
Rat
(rn6)
chr1:264742932-264745993 
ALTERNATIVE
RnoINT0132991
(Sema4g)
Cow
(bosTau6)
chr26:21681208-21684082 
ALTERNATIVE
BtaINT0130866
(SEMA4G)
Chicken
(galGal4)
chr6:22631356-22631426 
LOW PSI
GgaINT0043515
(SEMA4G)
Chicken
(galGal3)
chr6:24519140-24519210 
LOW PSI
GgaINT0043515
([1])
Zebrafish
(danRer10)
chr12:33755297-33758904 
ALTERNATIVE
DreINT0132756
(sema4gb)
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"