Special

MmuINT0147289 @ mm9

Intron Retention

Gene
ENSMUSG00000024485 | Slc4a9
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 9 [Source:MGI Symbol;Acc:MGI:2443384]
Coordinates
chr18:36688870-36689390:+
Coord C1 exon
chr18:36688870-36688983
Coord A exon
chr18:36688984-36689340
Coord C2 exon
chr18:36689341-36689390
Length
357 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
GATGTATGCCTGACTTGCAGAGT
3' ss Score
6.35
Exon sequences
Seq C1 exon
AGCAGGTAGTCAGTGGGGAGTCACTGAGCCCAGAACTGAGAGGACAGCTTCAGGCCTTGCTCCTGCAGAGACCCCAGCACCACATCCAGACCATGGGCATCAGGCCCTGCAGAG
Seq A exon
GTGAGAGATCCCTCTTTGGGCCTAGGATCAAGATTCTAGGGTAGGAGGGTCCCAGGGATCCTCTACGTTTTCTTGAGTCAGGAATGGGCTAACTTTGGCTCAGTCCTCAGGGCAAGAGAAAACTGGTGGTTACGGTAAGGGCAGAGGAGAGAGGGAGTGCCAGGGACTTAACAGCCAGGGCTCTCCCAAGGGCTGTATTTGGCAGGCACGGTGCTGGGAGTTCTACATGCTGCATCTTCTCATCTAATCTTTAGTTTCCATGGAGAAGTGTATTACAGCTATCCCCTAGCTAGGAAGCCCTGGTGGGCCTGCCCCTAAAGTGTGTGCTCTTAACCACGATGTATGCCTGACTTGCAG
Seq C2 exon
AGTCCAATGCTTTCAGAAAGGCTTCTCGTGATGAGGACGCCCCACTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024485-Slc4a9:NM_172830:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.765
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF075658=Band_3_cyto=FE(40.0=100),PF075658=Band_3_cyto=PU(2.9=10.3)

							
A:
NA

							
C2:
PF075658=Band_3_cyto=PD(9.5=52.9),PF075658=Band_3_cyto=FE(11.4=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000111358





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000073910, ENSMUSP00000095221
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr5:140361368-140361807 
HsaINT1042120
(SLC4A9)
Human
(hg19)
chr5:139740953-139741392 
HsaINT0153534
(SLC4A9)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr7:53243152-53244686 
BtaINT0136205
(SLC4A9)
Chicken
(galGal4)
chr13:975052-975142 
GgaINT1025764
(SLC4A9)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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






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