Special

MmuINT0006124 @ mm10

Intron Retention

Gene
ENSMUSG00000056004 | 9330182L06Rik
Description
RIKEN cDNA 9330182L06 gene [Source:MGI Symbol;Acc:MGI:2443264]
Coordinates
chr5:9437706-9440983:+
Coord C1 exon
chr5:9437706-9437843
Coord A exon
chr5:9437844-9440719
Coord C2 exon
chr5:9440720-9440983
Length
2876 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
TCTTTCTGCTCTCTTTCTAGAAC
3' ss Score
12.11
Exon sequences
Seq C1 exon
GATATAAATAGAAAAAGCACCAATGTGGTGGAATCATGGGGAGGAACCAAAGAAAAGCAAGCTTATACGCATGTCATATTCAAGAATGCAACGTTTACATTTACATGGGCGTTCCAGAGGACAAACCAAGGTCAAGAT
Seq A exon
GTAAGTCCCAACCATTTGCTTACTCGTTACCCCTGGGTATCATCTCCATTCAGAGCATAATGATGTCTTCTGTAGTCACTAAGAGTTGTACCCAGAAGCATCCTGCGCCCCATATACAGCATTATGAGATTGAAAGAGCATGTGTACTCTACACAAGTTGATATGAACTCTGTTGAGCTCATCACAAGCTATGTGCCGGTCAGCTGTGTTCTCTATATAAATAACTCATTCTGACCTGTATCCTGGAGTCCATAAATCATTCAAATGTACAATACAAACCCTTTGTAAGTGTACTATAAGCTTCATATGGGCATTATGAACTCTATCATGGAGATGTGAGATCAATGAATGAAATTTTGATTTCCCGTGTAGAGCCCCATAACCTGTATGTTAGCATTCTGTCTAAACCCCACCCCACAGTTACCTGGAAACAGCTAGGTTGGCCTGGTCAGGCCACTATAAAAGGGGCTGCACCCCTTCCTCACCCTCTTGCTCTCTTGGTCTCTTGTTTCTCTCTTGCTCTTTCTCTGTTTCCCTTCCCCCCACCTCTCTCCATGTGCTCTTGGCCAGCCTCTACTCCTCTACTTTTCTACTTTCTCTGTCTCATCTGTCTGTCTTTCTCTGCCTTTACTATCTTCTTAACTCCCCTCCCCATGCCCTGAATAAACTATTCTATACTTTACCATCATGTGGCTGGTCCCTCAGGGGGAAGGGATGCATGGGCCTGCTGAGGTACCCCCTTCCCCTATACCTCACCACACATCCATAGAATATGACCCCCTTCTCTTTACACAATGCTAACACTGTACATAGGATACTATAAATTCCATTCAGAGAACAGAGAACCTTAAAGTTCCACCATGAGATGTACACAGTATTACACTTACTATACAAGATAATATAATCCCATAGTTTTATTTCTTTTACAATGCAAAGATGATGCTCACTTGTGGTGATGTATATAAAACTGACAGTAATTTGAGTCTGTCATCTTGTTATATAGTAAATTGGTATAAAAATCACAATTTTTAATCTTTTTGAGAATACGAATGTATGAAATGGGTGGAATAACAACAGACCTCTTTTATTTTGAGTGATGAGCAAATACAGTTGTTGAAGCTTATAAGAAAATTCCATTTTGATTTTACTTAAACCTTAGTTTTTAAGTCTTTAGGAGACCGAGAAGCTTCCTAGCTTCCTTCTCCTTTATCCACCCAGTAATCTTTGCTTAAGAGTCATTAACTAGTGTGGGTTTATGTTTTTCATTATGATACTGTCTTGTTTTAGAAAGAATGCATTTGTATATGGGATGGTAGGACACAGCCAACCATTGCCTTTCTTTGATTTTCATTTTTAGCATAGACCTAATCATCTCTATATGTGTCAATATTAGCAGAGCTGGTATATATGTATATATGTATGTATTTTGGAGTGTATGTGGGGGGGGTACATACATGTGTGTGTGTGCTATTTTTTGATTGTGCTTGTGTATCTGTGAATGCGTGTCTGTATGTAGATCAGAAACAGCATTGGAAGTCATCTGATTATTCTCAACATTATTTTTTTTGAGACAGGAACTCTCAGAAAAATCTAGCAACAACTATTGTGGCTTGACTAGCAGGCTAGAGAGCCTCCGGGATATCTGCCTCTGTGCCACCCAGTGCCACATCACTGGGGTTAGAAGCCCATGGTGCCATACCCAGTTTTTATCTCATTGCTTGGGAGCTAAACTCGGGTCCTGATGCTTGTGACATAAGCACCTTGCCATTGCACCGTGTCCCTAGTCTCAGGCATGGTATTTGTTGTGTATCTCCACAGTTGTGACTTGATCAAAAGGAGAACAAGGTGGATCTTTGCTTGGAGTAGCTTCATTGCTGTGGTGGCACGTGGGGTTCATTTTTCTCTTTTCTCTTCAGATGTTCAGTGGGAAGCAAGTCCCCAGATTTTTCAAGACTTCACGTTGTTCCTTGGGGGGTTATTATTTAGTATTCAGAATATAAACATGAGGGGGTGAACACAGATGGAACTCCATTTTCTCTTTGTCTTTTCTTTTTTTTAAAGATTTATTTATTATTATACATAAGTACACTGTAGCTGTCTTCAGATGCATCAGAAGAGGCCATCAGATCTCATTATGGGTGGTTATGAGCCAACATGTGGTTGCTGGGAATTGAACTCAGGACCTTCGGAAGAGCAGTCAGTGCTCTTACTGCTGAGCCATCTTGCCAGCTCCCTCTTTGTCTTTTTATCTTGGTTCAGAAGAGCATTAAATAGTCAGATGTGACATTGTACACTAGGGTGACAAAAACCTGACCTTTGTTAATCTTATACAAAAGGAAAAAATGAGGCATGAGTCAGCATCTTGCTTGCTCCTTTGACATCTTTTTGATAGAAATTCAAACGCATTGCTTAGGAGAAGGGCTGAAGAAGGAAAGAAATGCTCAGAATGGGTCTATCAGTATCTCACAGTGTTTGAGTGATGAAAAGAGGGCCTTACCTTCCAAGATTTTCCACCCATCCAGACTTTCAGCATCAGACCGTATCATTAAGAATTATGCCTGGGTAAACCAAGGTGAGATATAAAGCTACTCTGCTATTGTCTTGGATACAGTCTGTAACTGTGCCAGTGCCAATTATGATGTGTCTGATGTCAACTGCAGCAACACATCTGGAATTCCATGGTTATAGAAAGTGGCTTCTAATGTCAAGATTTAAGGGCTTTTATTTAGAACTACTGAATGGGAGTGAAGGTAACCCACTGTTACTCAAGCTGTAGTCTGGAACACTCTGTTTATTCTGGTGGTGTCAACAAAAGCATAACTTGCTCATGCAGTTGCACTCCAAGGCAGATGCCACTCTTTCTGCTCTCTTTCTAG
Seq C2 exon
AACAGACGATTCATCAATGATGTGGTGAAGATTTATTCTATCACAGCCACTAATGCAGTTGATGGGGTAGCAGCGTCATGTCGTGCCTGTGCCCTGGGCTCTGAGCAGTCGGCCTCATCATGTGTACCCTGCCCCCCAGGCCACTACATTGAGAAGGAAACCAACCAGTGCAAGGAGTGTCCAGCTGACACCTACCTGTCCATCCACCAGGTCTATGGCAAGGAAGCTTGCATTCCGTGTGGGCCTGGAAGTAAAAGCACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000056004:ENSMUST00000069538:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.008
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF076998=GCC2_GCC3=PU(80.4=46.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000069165





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000120849, ENSMUSP00000121757
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr7:86913205-86914722 
LOW PSI
HsaINT0086703
(KIAA1324L)
Human
(hg19)
chr7:86542521-86544038 
LOW PSI
HsaINT0086703
(KIAA1324L)
Rat
(rn6)
chr4:21610311-21613013 
LOW PSI
RnoINT0122542
(RGD1563349)
Cow
(bosTau6)
chr4:33723995-33725719 
BtaINT0081111
(KIAA1324L)
Chicken
(galGal4)
chr1:7500079-7500865 
LOW PSI
GgaINT0113146
(KIAA1324L)
Chicken
(galGal3)
chr1:8104463-8105248 
LOW PSI
GgaINT0113146
(KIAA1324L)
Zebrafish
(danRer10)
chr4:9681411-9681476 
LOW PSI
DreINT0142748
(si:dkey-153k10.9)
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • 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"