Special

MmuINT0147229 @ mm9

Intron Retention

Gene
ENSMUSG00000021733 | Slc4a7
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 7 [Source:MGI Symbol;Acc:MGI:2443878]
Coordinates
chr14:15589799-15592855:+
Coord C1 exon
chr14:15589799-15589945
Coord A exon
chr14:15589946-15592748
Coord C2 exon
chr14:15592749-15592855
Length
2803 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TATATTTTTGTGGAATTCAGGAA
3' ss Score
6
Exon sequences
Seq C1 exon
ATTTTTCATGATGTGGCTTATAAAGCAAAAGATCGTAATGACCTCCTATCTGGAATTGATGAATTCTTAGATCAAGTAACTGTTCTTCCTCCAGGAGAGTGGGATCCTTCCATACGCATAGAGCCTCCAAAAAGTGTTCCTTCTCAG
Seq A exon
GTAAGAGTCTAGAGATGTACTTCTGGGAGTTGTTTTCTTTTTTTAAGTTAAAAACTTTTCATGAAATATGTAAGTTATGCATTTTTATGACACAAAAATTACAGCTATTTACAGTGGATGTGGCTAAGTAAGAACTCTTCTTTAGCATTGAATCCTAGCACTGAAAGTAAGTCAATAGTGATCAGTGGTGGTGCATCAGACAGGATGTACCACTGTCACCATGCCCCCTGTACATCTTTATCCCAAACAGATTTGTTGATTGTTAGTTGTGTTGTTACCCAGACATGTAGATATTTGTAGTCTGCCTGCTTTTTTGTTATTTGAGTAAATTTAGGTAAATCATTGTATGTATATATGTATGTATGTATGTATGTATGTATGTATATATATATTGAATCTACATGTGCTATTACTAGTCCATTTGTATCACAAAAACAAATAACTTTGGGGTACTGGTTCTTGAGCAACTTTTAAACAGTATGGAATAATTTGTTTTTGCACATTTGGAAAATTTCTGGCATACATTTTTGAACTATATCACTTGCCAAGCATAAGCTTTAACAAGTTGCCTGTTTCTTTATGAAAATTGCCTTATGTGAGTTTCCCCCCCCCCCTTAGGTCAGTTCAGTTCTGATTCATTTTGTTTGCCTGGTATATTACCCATTTACTCAGATAAGTTTATCTATTACACTCCCTTTGATTTGTGATGTTCCGTCCTGACCTATGTTTAGTTTAGCTAATAGACTAATAATTTATTATATTTTTCAAATAATAATTTTTTAATGTGGATCTTTTTCTACTTAATTTCTGCTTTTAGCTGATTTACTTCACTCCTACTATCCTTCCTAAAGATTTATTTATAATTTTAGTATATTTAATTATTTTGTTTGTTTGTTTTAGATTTATTGTATTTCATACACATGAGTATTTTGCTTGTGTAGATGAATATGTACCACAGGCATGCCTGGTACTCAGGATCAGATAAGCCAAAACTGGGATTATGCATACTGTGAGCCACCATGTTAATTAATGGTGGCAATTGAACTCAGATCCTCCGAAGAATAGCCAGTGTCTTAACTGCTGAGCCATCTCTCCAACCCCCATCTTTTAAAATGTTTCCTAAAAGAATGTTTGGTTTGGTTTTGTTTCGACACAGTGTTTTACTGCATAACTTTGTGTGCCTGAAACCTTCTTGTAGCCACACTGTTTAAATTTGAAGTGTCTTGCCTTGGTGTCTCAAATACTAGAATTGTAAGCATGAGCCACTTCCTGGTGTCTTTATATTTTCATATTGTTTTAGATACTACTCAGATTATAATATTTAGTATGGAATTCCCTTGTCCTGTAATGTGTTCTGTTTCCTCTTTGATCTAAGATACACATTGGTTTTATCTTTGGCGTTTTCAAGTGTGACCTTACTTTTGTAATCTTGCTACTCTGTGTTAATATGATGTATGTCTAGGTCCATGGGAGCCTTGGACTTCAGGGGCCTCTTAGGACTACATGTCTCTCTGTTTCCTTCATATTTCATTTCCTCCCTCTTTTTATTATATGTGCTTATCTGCACAACTTGAAATATTCATTTTGTGTTAACATGGGGGAGAACATTCTGTATTGTAGAAGTAGTATTGTTTGCTTGTTTGTTTTGATTTTTAAAATGAAATATAAGAGCCAGGCGTAGTGGCGCACACCTTTAATACCAGCACTCGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCAGGTCTATGAAGTGAGTTCCAGGACAGCCAGGGATATACAGAGAAACCCTGTCTCGAAAAACAAAAACAAAAAAATGAAATATAAGATGATACTGAAGGGATTTTTGTGTTGCTTTTCTAAGAAAAATACTTTAGTAATTGGTTTTCTTTCTCTTTCCTTCTTCCTTCGTCCATCTTCTTTTTGAACTTGTAGCCTAGATTGATCTTGAATTTACAGTATTCTTGCCTCAGCCTTTTGAGAGCTAGCAGTTTAGGTTTGTGGAAAAAGGTAGTAACTTTAAAAATTGATGTAAAGTTTGGTAGTTAACCATAGTATTCTAAATACTTTGATGAGAAATGTGTTTCTTTGGGAGAGTGTTCATAGCTAGGCTGGCTAGTGTTTTGTCAAATTAATACACGCTTGGGCTATACAAGAAGAGGAGGTCTTACTTGACAGGATGCTTCCATAGTCAGGACTCTAGGACATTTTCTTGGTTGATACTTGGTGAATGTGAAAGGGCCTAGCTCATTGTGGGCAGTGTCATCCCTGGACTGGTGGTCTTGGATAGTTTAAGAAAGCAGGCTGAGCCAGCCATGAAACACAAGTAAGGAGTGTTCCTCCATTGTCTTTGTTCCAGTTGTTGCCTCAGGTTCCTAGCCCTTACTTCCTTCATGAAGGACTATGATCAGGACATATTAGCTGAAATAATAAAGCCTTTTCTTCCCCACGGTGCTTTTGATCATGGTGTTTTATAACAGCAGTGGAAATTTAATAAAACAATAGCTATTATAGAATAGAAATTTGACATGGCTTCATGAATATATCTTATAGTGCTTTGATGTTAGAAGATAGTTAAGAAAGCTAACTATAAATTTAAAATATGAACAGAAGTTGATAGTCAATTCTAAATTCATCTTTTAATTGTTATTGTTTTAAAAAGTTATACTAGGAAACTTTATTTTCCCCCAGAGAGTACTTGGGTAAAATCTTTATGAATGTAATATTCCCTCTAGCCGTCTCAGATGCCAGTTTTCTTAAAATTGAATTCTGAAAATATATTTTTGTGGAATTCAG
Seq C2 exon
GAAAAAAGGAAGATTCCTGTGTTTCCTAATGGATCTGCTGCAATGTCTGTTGACCCTCCCAAGGAGGATGATCACCATGCTGGGCCTGAGCTGCAGAGGACTGGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021733-Slc4a7:NM_001033270:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.163 A=NA C2=0.500
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF075658=Band_3_cyto=PD(13.4=73.5)

							
A:
NA

							
C2:
PF0095516=HCO3_cotransp=PU(1.2=16.7)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000058313f1079A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000058313, ENSMUSP00000088071, ENSMUSP00000128870
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr3:27411749-27418485 
ALTERNATIVE
HsaINT0153476
(SLC4A7)
Human
(hg19)
chr3:27453240-27459976 
LOW PSI
HsaINT0153476
(SLC4A7)
Rat
(rn6)
chr15:11866283-11868928 
ALTERNATIVE
RnoINT0138543
(Slc4a7)
Cow
(bosTau6)
chr22:1792035-1803879 
LOW PSI
BtaINT0136141
(SLC4A7)
Chicken
(galGal4)
chr2:39041025-39042257 
ALTERNATIVE
GgaINT0101748
(SLC4A7)
Chicken
(galGal3)
chr2:38457589-38458821 
LOW PSI
GgaINT0101748
(SLC4A7)
Zebrafish
(danRer10)
chr16:42814095-42814645 
LOW PSI
DreINT0151585
(slc4a7)
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"