Special

MmuINT0147060 @ mm9

Intron Retention

Gene
ENSMUSG00000006574 | Slc4a1
Description
solute carrier family 4 (anion exchanger), member 1 [Source:MGI Symbol;Acc:MGI:109393]
Coordinates
chr11:102218031-102218565:-
Coord C1 exon
chr11:102218355-102218565
Coord A exon
chr11:102218244-102218354
Coord C2 exon
chr11:102218031-102218243
Length
111 bp
Sequences
Splice sites
5' ss Seq
TAGGTACAC
5' ss Score
4.06
3' ss Seq
TTTCCTTTCCTCTACAACAGACT
3' ss Score
9.04
Exon sequences
Seq C1 exon
GTGTTCCGCATTACCGCCTCCATGGCGCATAACCGAGAGGAGCTGCTGCGCTCTCTGGAGAGCTTTCTGGACTGTAGCCTGGTGCTGCCGCCCACAGACGCCCCTTCAGAAAAAGCTCTGCTTAACCTGGTACCGGTGCAGAAGGAGCTGCTTAGGAGGCGGTACCTGCCCAGCCCCGCCAAGCCAGACCCCAACTTGTACAACACTCTAG
Seq A exon
GTACACGGACAAGGTTTCTTGATTCCCCCATGGGGCCCTGGATCCCCAGTACACTGCTCCTTTCCTCGCAGACATTTGCCCCTCTGACCATTTTCCTTTCCTCTACAACAG
Seq C2 exon
ACTTGAACGGGGGAAAAGGGGGCCCTGGTGACGAAGACGACCCTCTACGGCGCACAGGCCGGATCTTTGGAGGCCTGATCCGTGATATCCGGCGCCGTTATCCTTACTACCTGAGTGACATCACCGATGCGCTCAGTCCCCAGGTGTTGGCTGCTGTCATCTTCATCTACTTTGCTGCCTTGTCACCTGCCGTCACCTTCGGCGGCCTCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000006574-Slc4a1:NM_011403:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.085 A=NA C2=0.194
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF075658=Band_3_cyto=PD(14.8=50.7)

							
A:
NA

							
C2:
PF0095516=HCO3_cotransp=PU(29.7=79.2)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000006749





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr17:44258181-44258412 
LOW PSI
HsaINT0153296
(SLC4A1)
Human
(hg19)
chr17:42335549-42335780 
LOW PSI
HsaINT0153296
(SLC4A1)
Rat
(rn6)
chr10:90304123-90304243 
LOW PSI
RnoINT0138374
(Slc4a1)
Cow
(bosTau6)
chr19:44699013-44699214 
LOW PSI
BtaINT0025639
(BEB3)
Chicken
(galGal4)
chr7:21508237-21508298 
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr2:32429416-32429517 
LOW PSI
DreINT0151500
(slc4a2a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CGCCCCTTCAGAAAAAGCTCT

				
R: 
GCATCGGTGATGTCACTCAGG

				
Band lengths: 
243-354

			

		

	





	
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"