Special

MmuINT0037297 @ mm9

Intron Retention

Gene
ENSMUSG00000007041 | Clic1
Description
chloride intracellular channel 1 [Source:MGI Symbol;Acc:MGI:2148924]
Coordinates
chr17:35192172-35195664:+
Coord C1 exon
chr17:35192172-35192353
Coord A exon
chr17:35192354-35195274
Coord C2 exon
chr17:35195275-35195664
Length
2921 bp
Sequences
Splice sites
5' ss Seq
CAGGTTGGT
5' ss Score
8.08
3' ss Seq
GACCTCTCTCTAACCTTTAGGTG
3' ss Score
10.28
Exon sequences
Seq C1 exon
ACCTAGAGAAGGGACTCCTGAAAGCCCTGAAGGTTCTAGACAATTACCTGACATCCCCCCTCCCAGAAGAAGTGGATGAAACCAGCGCCGAAGATGAGGGCATCTCTCAGAGGAAGTTTCTGGACGGCAATGAGCTCACCCTGGCTGACTGCAACCTGCTGCCAAAGCTTCACATAGTACAG
Seq A exon
GTTGGTGGTCACCGTGGGGGGAAACGGGATCAATCTCTAAAGTGATTTTTTTTTTTTTTTTGAGACAGGGCTTCTCTGTGTAGTCCTAGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGTGTGAGCCACCACGCCCGGCGGTGATTTTTTTTTTAATCACCTTTTATTTATTACAAAGGGCAAAACACAAACGGGGTTTGGAAATCAGGAGAAAACTGGGGGGAGTCAGTTTTCTCCCCTCCACCACGTGGATCCCAAAGATTGAGCCTTGGTCACCTGACTTGGCTGCAGATGTCTTTACTCTGCTGAGCAGTCTTACCAGTCCAGTGTTGCTGTCCATCATGCCTAGGCTTTTACGTGGATGCTGAGCATCCGAACTCAGGCACGCATACTTGCACAGCAAGCATCCACTTTCTCCGAATGGTTTCCATAGATTGCTACCAGTGATGGGCCCCTGCCCAGGGACCACACCCTTAGCAATTGTTGCCCAAGTAAGAGAATTACATCCCATGACACAAGCCATGCTTATACAGCATCCATTAAAGAGTGGCATTCAGTTTTACTGTATGTCTGTGTTTTATCTGTGTACATGTGTGTCTGTATGTGCCTGTGTATCTGTGTGCATATGTTTGCCTGTGTGTATGGGTGTCTGTATCTGTGTGTGCCTGTGTGTATGTGTGTGCCTGGGATGTGGGGGAGGGTGCGCCTGTGTGTATGTGTGTGGCTATGTGTCTGTGTGTATGTGTGTGCCTGCCTGTTTGTATCCAGGGTTGCTTCCAAGAAGGCTTTTCCTGCAACTGTATCACTGCCAAATGTACAAATCAAACAAAGGATTCTCCCAGGTCTATGATGTAACTCTTCACATAGTCCAGGCTTCCCAGGTTCTCTCAAGGACTCTTCCTGAGTTGCTGTTTCCTTTCTGTCCTGGCCTTAAAGTTACAGTGTAATTTAGTAAAACACAGAGCCACTATCACTCCACCATCAACTGAGAGGCACCAGACAGTAAGAAAGCTGGGCAGAGCGTCTCCTCTCCTGCCTGTAATCCTCAGCGTGCTGCAGGCTGAAGTAGTAAGTTCAGTGCGAGTTGGAGGCCAGCCTTAGCTACAGAATAAGAGCCTGGTTCAAACACCACCACTACCACCACTACCCCACACACACAAAGAAAAAGAAAAAAGAGAAAGCAGCCAGGCAGTGGTGGCGCACGCCTTTAATCCCAGCACTCAGGAGGCAGAGGCAGGTGGATTTCTGAGTTTGAGGCCAGCCTGATCTACAAAGTGAGTTACAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTTGGAAAACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAGAAAAGAAAAGAAAGCAACGAGAAAAGAAGCAAATGATGTTCATTTAGTTCTTGCCCACAAACAGTTGAAATTGAATTGAAGAGAAAGCATTCACATCAAGGGATGTGATGGCTTGCAGAGATGGCTCAGTGGTTAAAAGCACCGGCTGCTCTTCCAGAGGATCTGGGTTCAATTCCCAGCACCCACATGGCAGCTCCCAACTGTCTATAACTCCAGTTCTAGAGAATCTGACATCCTCACTCAGGCATACATGCAGTCAAACACCAATGCACAAAATATAAAACAAACAAACAATTAAAAAAACCCATCCACATCAAGGTACTAAAAGATGACCTGAAAGAAGTCAAGTGAAAAGGAGACAAAGTTCTCTACAAAAATGTTTACTCTTTGCCAACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTACTGATAATGGAGCCCAGGACTAACCACAACCCTAGCCTGTGTTTGTCTCTGCCTCTGTATATATTCAGTTTTAATCACACGTGAGTGCAGGTGCCTTTGGAGTGCAGAAGGCGGTGGTAGATCCCCTGGAACTGGAGCTGCCCACTGAGGGCGCTGGAAACCAAACATCTACAGCAGGTGTTCACCACTGAGCCATTTCTTAGCCTGTCTCTCTCTTTATCTGTTTCTTGAGACAGGGTCTTTCTATTTAGTTTTAGTGACCATGGAACTTGCTAGTGAGTTCTAGGACTGCCAGGTTTACACAGAGAAACCCCATCTTGTGATGTGTGTGTGGGGGGGGAGGGGGTAGTGAGGATGGGGATGGAAGGGAAAGAATCGGTGAGAAGTCTCTAGAGGGGCTGGCTCAGGGGTTAAGAGCACTGACTGCTCTTCTTGAGGACCATGTTCAGTTGCCAGCACCCACATGGCACCTAACAGCATCTGTAACTCAGACCAGAGGATCTGATGCACAGTCATACAAATAAACAAACGCCCATCCTCATAAAATAAAAATAAGTCTAGCCAGCATGGTGGTGCACGCCTTTAATCCCAGCCCTTAGGAGGTAGAGATGGGTGCATTCCAGAGTTTGAGACCAGCCTGGTCTACAGAGCAAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTTGAAAAGCCTAAATAAATAACATCTAAAAGTACAATTTTTAAAGACTCTAGGCACAGGGTACATGTCTGTAATACCATTCCAGAGATCATCCAGCCTGCGTGACACAGAGAGACCCTATCTCAAAAGAACGGCAGCAAAAAAGCTTGTAAGAATCGAAGTTCATTGGTCTGGCATCCTGGACAGGGCTCGGTTTTTTGTTTGTTTTGTTTTGTTTTTTGTTTTTGTTTTTTACCTGGCAGACCCTAAAGGAAGAGAAAGTTCAACAGCTTCAAAGCAAAGCAAGCATGCCTTCCCTGGGGCTAACACACTGACCTCTCTCTAACCTTTAG
Seq C2 exon
GTGGTGTGCAAAAAGTACAGAGGCTTCACCATCCCAGAGGCATTCCGTGGAGTGCATCGGTACTTGAGCAACGCTTATGCCCGGGAAGAATTTGCCTCCACCTGTCCAGATGATGAAGAGATAGAGCTAGCCTATGAGCAAGTGGCCAGGGCTCTCAAATGAGCACTTTTTAAAGGGTCCTTCACCCACTCTGTGCTCTCCACAGAGGCTTCGGGGGGCTTCCACGTTGCTGCATAATGGACACACTCCGAAATTGCCAGTGGGCAGGAAATCCGGGGCACTTGTGGGGTGGGGCTGTGGGATAAGGCAAAGGATAGTGGACAAGGGTAAGATTTTTATTTTGGGATGGGGTGGGTAGGACAACGCATTTCAGTAATAAAATACAGAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000007041-Clic1:NM_033444:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.197 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF134101=GST_C_2=FE(66.7=100)

							
A:
NA

							
C2:
PF134101=GST_C_2=PD(25.6=42.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000007257





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:31731004-31732216 
LOW PSI
HsaINT1007846
(CLIC1)
Human
(hg19)
chr6:31698781-31699993 
Rat
(rn6)
chr20:5045457-5048772 
LOW PSI
RnoINT0037274
(Clic1)
Cow
(bosTau6)
chr23:27397277-27398542 
LOW PSI
BtaINT0039274
(CLIC1)
Chicken
(galGal4)
chr4:1803004-1803085 
LOW PSI
GgaINT0077362
(CLIC2)
Chicken
(galGal3)
chr4:1801164-1801245 
LOW PSI
GgaINT0077362
(CLIC2)
Zebrafish
(danRer10)
chr19:17477059-17477137 
LOW PSI
DreINT0047529
(clic1)
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"