Special

MmuINT0105100 @ mm9

Intron Retention

Gene
ENSMUSG00000036062 | N28178
Description
expressed sequence N28178 [Source:MGI Symbol;Acc:MGI:2140712]
Coordinates
chr4:42947505-42950791:+
Coord C1 exon
chr4:42947505-42947690
Coord A exon
chr4:42947691-42950712
Coord C2 exon
chr4:42950713-42950791
Length
3022 bp
Sequences
Splice sites
5' ss Seq
TGTGTGAGT
5' ss Score
5.84
3' ss Seq
TCCGCTTCTACTTTCTTCAGGAC
3' ss Score
9.64
Exon sequences
Seq C1 exon
GTTGTCAACGACGAGATGTGTGACGTCTGTGAAGTCTGGACCGCTGAGAGCCTCTTCCCATGCAGAGTCTGCACCAGGGTTTTCCACGATGGTTGCCTGCGCCGCATGGGCTACCTCCAAGGGGACAGTGCAGTGGAGGTGACTGAGATGGCCCATACAGAGACAGGCTGGAGCTGTTACTACTGT
Seq A exon
GTGAGTCTGGACTGCAGGACAGGGGGAAAACTCGGTGTTCATCCCAGAGAAACTCTTAAAAGTGACTGTTTCTAAGTAGTGACCTAAGGGGCTTTTCTAATAGTGCATGCAAGGGTCCTGGAGCTAGAGGTGCAGTATATGGCACTTTTAAAACATGCCAGTAGCAAACAGGCCCAGTTGTAACACAGCAGACCTTGCCAAGTATGTTCCAGAGGGAGCAAGCCACCCTCGGTTAAGAATCATAAAAAGAACAGGCCTAACCTATCACTAGTCATTCTGCATGGGGCAGTGCTTTCTCTACAAGCCTGTGCCTGCCATTCCTTGTACTCATCTGAGAAACCAACCTGGCATCCTGAACAGCTCGCTTCCAGCAGAGGGAGATTCTGTTCCGGGAAAATACTTAGTCCCATGGTCCTCGCTTGACCTGCCGCCTGTTAGAAGCCTTTGTTCTTCGCCTCTGAAGTAATCATTATGTGAATTAAAGAGCAACACTGCATTGATTCAGAACTCTGAAAACCATATATAAATACCTTCCAACTTCTAATGGCAGAAAGAGTCTAAGGTTTCTGCTGAAAGCCGGATTCATAGCCATTTATCATCATGCCTGCGTGGAATCCAGGACTTCCCTGCCTGCTGTGCGGATGTCTTCCCTACTCTCTGGTTCGGTGTAAGGAGCAGCTGGCAACTGTCTTCTTCCACTGTCTGCAGAAAGCAGATAGGTGCTACTTTCTGACTCTCCATCTATGGCTAATCCACAAAATGAAGCCTACAAGTGACTTCCAGCTCCCGAAATACCTTCCCTGTAGAATATGCCACACCAGACTCTGTGCTACAGTCTTTCCCTCCACTTCTGCCCCAGTCTGTACACACACGCACACGCACGCACGCATGCACGCACGCACGCTTGCCAGTACGCTGCCAGCATGAGCCTGGGTCAATCTGTGTCCCTCTTCTGTCTCTCGGGCACTCTCTGCTTCCTTCCCAGCTCGCTAGGGGCCAGCTGCTGCCACCACCTCCACGGGCCTTTTGCACACCCTTCCTTCCAGTTCATCCCTTTCTTTTCCCTCCACTCACAATCACACTTCTTAAGAGCGTTTCACAGCCTCCTGACTTCTCTGCCCTGCAGTGTGACCTCGGCCGTCAGCACTTTGTTGAGTTGGCTTGTGTTGAGCCCACCGACAATCTTCTGTTTCTCAGGCATCTTCTTAGTCAGTCTTTTTCCTTGTTTCCTCCTCTTTCTCCTGGCAGTTAGGTATTTTCTAGAATTTATACAATATATGCAAGCTAGAGAAAGTGTTTCCAAATAACGAATCCCCGGATGCGTGTCTGACCAGTGCTAGCACCGCCCACTATGCCATGCCACAGCTATGCTATGCCATGCCCAGTCTTCGCTTGGTACCCAGTACTCCCAAGGGTCTTCCAGCCTTCTCTGACCTCTCCTCCGCACCCGTGGTTTGTTCCAGTTCTAGATGCTGTCTGTATTCCTCAGGATTCCATTGTCTTTCCCACTGTATTCGTTGTCTTCGAGTGACTTTGTCCTATAACCTACAATCAAATTATTAACGATGCCCGTATCGGTGCCCAGACTTAAATTTCCTGTCTCAGGGGCTTATCCATCTTGATGTCTCACCAGTACTTCATGCTCAGAATGTACCGAAATGAACTGATGTCCCTGCCTAAGCCTGCTCTTTCTCCATTCCTTTCTTCTGTGAGCAGTAGTATCTATCATTCCCCAGTTTCCCACCCCCCACTCTTCCGGTACCCTCCCTCATCCCCCACTGCCGGTACCCTCCCTCATCCTCCACTGCCTGTACCCTCCCTCATCCCCCACTGCCTGTACCCTCCCTCATCCCCCACTGCCGGTACCCTCCCTCATCCCCCACTGCCTGTACCCTCCCTCATCCCCCACTGCCTGTACCCTCCCTCATCCCCCACTGCCTGTACCCTCCCTCATCCCCCACTGCCGGTACATCAGCAGGTTCAATGACCTCTGACACCTCTCGCTTCTTCCCTCCCCTGTCCGCTGGGTTTAGCCACCTGCTTTTTCTTACCTGTGCCTCTGGAACAGCACCCAGCGGCGATCCATACCACCAGATTTTGCTCTTCTAATCTGACCATGACAGCTGCCCCTCTGTGCCTCCTCAATGTCCTTAGAGTAAAAGGTCTGAGTTACGGGGCCCCGTCAAGGCCATCTGAGGAGTGTCACAATTCTTCATTTCGAGTTCTCCCCGATTGCCTTCACACTCACATGCAGCAGCCACACAGTACCAAACATCCCAGTGCTGTGCACACTCATGTGCCCAGGACACGCCAGGCGCTCGGTGACAGAACCATAGGATTGCTTGTGAAACTCACGCCATGTCTGAGTCTGCTCCTGGCTGCTATTTTAGGAGGAAAGTTAACTAATCATTACAAAGAACCTTCAATAGTAATGCTAACAAAATAAGACCTCAATGCTGCTTTAGTAATTAAACTCCTATGACACCATAAAAATTGGTTTTGTTTAGGGACATTTCAAAACCCATTCTTGAGCCATTTAAAGTTGCACAACCCACTAGAAGCAGGGCTATTTGTTTTTTATAACTAAAATGTGCTTTAAGCCTGGCCACAAAGCCAGTGGACATAAAATAAACACATACTGAGCAGCTGATGGGTGGAGCTAGGACCTACAGCTGAGTACCTGTCTCTCTTTACACCCACAGCAGCTTTGGGGGTTGCTTCTGTGGCATCCCTAGGGCAGTTCACAGGCTAACTTGGAAGCAGGTATTGAATAAAGAGACTGGACTAGAGCCAGGATAGCTGGATTTTAGGGGGGTGGGGTTCATCCCTAGAGTCACTCAGCTCCAAGCAGATCTTCCCTCTGTCTGGCGCCCCAGTCTCCTTGACAGTGGCTGGGTGGTTGGGATCGTGGGTTTTACCTCCTCTCTGGTGGAGGTGCTGTTTCCGTCTCTCTTGATCCTTAGCGTTTCCCTTGTCACTGGCCTGTGTGGCCACTAGCTAACTCCGCTTCTACTTTCTTCAG
Seq C2 exon
GACAACCTTAACCTGCTGCTTACTGAGGAGGAGATGTATAGCCTTACTGAGACCTTTCAGCGGTGTAAAGTCATCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000036062-N28178:NM_172690:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.015 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0013017=C1_1=WD(100=91.5),PF0062824=PHD=WD(100=68.1)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000103609





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000071011, ENSMUSP00000103610, ENSMUSP00000115816
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:34972532-34976151 
LOW PSI
HsaINT0086388
(PHF24)
Human
(hg19)
chr9:34972529-34976148 
LOW PSI
HsaINT0086388
(KIAA1045)
Rat
(rn6)
chr5:58378180-58381002 
LOW PSI
RnoINT0110442
(Phf24)
Cow
(bosTau6)
chr8:59671031-59674230 
LOW PSI
BtaINT0081013
(KIAA1045)
Chicken
(galGal4)
chrZ:8366068-8366226 
ALTERNATIVE
GgaINT0063023
(PHF24)
Chicken
(galGal3)
chrZ:7895140-7895298 
ALTERNATIVE
GgaINT0063023
(KIAA1045)
Zebrafish
(danRer10)
chr10:17933579-17953747 
LOW PSI
DreINT0139665
(si:ch211-269m17.1)
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"