Special

MmuINT0147209 @ mm9

Intron Retention

Gene
ENSMUSG00000068323 | Slc4a5
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 5 [Source:MGI Symbol;Acc:MGI:2443220]
Coordinates
chr6:83227507-83230158:+
Coord C1 exon
chr6:83227507-83227565
Coord A exon
chr6:83227566-83229957
Coord C2 exon
chr6:83229958-83230158
Length
2392 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGC
5' ss Score
8.69
3' ss Seq
TTCTGTGCTTGGTCTCCAAGTAC
3' ss Score
3.36
Exon sequences
Seq C1 exon
TGAACACAACCACGGTCAATGCCTCAGCCCCACTGGCACCAAACACCAACACGTCTCTG
Seq A exon
GTAAGCCTCTTCCTTCCAGGGCAGACTGATCATGCGGTTTTGTTTATGGTGGGGAGTCAGGAAGGAGTTGGGAGGTGAGTCCCAGGAGCACATGGGTTCTGAGAACGATGTTTTTAGTTTGTAACCGAAAGCATCCTATTCTACAGCATCATCAGTGCGTGCCTTCTCTATGCAGAACGATAGCATGTGCATTCCCAGGGGAGGCCAGGAACAGAGGTACACACATATATGCACAGGTCTGCCTGGAAACCACCAGTTCCCATCCAACAGTGCACTTCCAGCACCCAAGGTTTATTAGACTCCCCCTGCTCAATGAATTTGATCAGCCTTTTGGCTTAATAGCCTCCAAGGACCTTAGCTGCCCTGCCTTCCTGAAAAATGGGAAGGAAGTGTGGGCTGTAGGCCTCTCCAGCCTAAGTAGATGGAAGGATGCAAAATTATAATCCAGGTAAAGGGGAGCATGTAGCCGTGGGGCAGCTTTGTAAGCCGTGAGTGACCTTAAGGTTGCTCAAGTTCCCTTGCACAGGCAACTAATGGCTCAGTTCATATCTACCTCAACTGACTATTAGCCAAAAATGTTCACACATAAGACTTTGAGAAGAGCAGACTGGGGCAGTGCCTACCTGCCAGTGCCTGTTTTTTTTTTTGTTTGTTTGTTTTTGTTTTTAGATTTATTTATTATTATATCTAAGTACATTGTAGCTGTCTTCAGATGCACCAGAAGAGAGAGTCAGATCTCATTATGAATGGTTGTGAGCCACCATGTAGTTGCTGGGATTTGAACTCAGGACCCTCAGAAGAGCAGTCGGTGCTCTTAACCACTGAGCCATCTCTCCAGCCCTGCCAGTGCCTGTTTTATGTAAGGGGCTATGTGCTGGGATCTGGGCTCCAATGGACCAGCTGGGATGCTTTGGTCTGTCTTTACATTGGCTTTTCAGTCCTTACCTTCACGTGATAAAGCACCCTGGCAAAGGAAAACCGTTTTAAGGGAGAAAGGGTTTATTCAGCTCCCAGTCCTAGGCTGCAGTTCATCACTGCAGAGAAGGCAAGGCGACAAGCACTTGAAGCAGTGAGTCGTGTGCACCCAGTCGGGAATGAATGCATGTATGCTCTACTGGCTAGCTGGCTGTCTCCACTCTTACACAGTCCAGGATGCACTGTCTAGGGAATGGTGCCACTTATGGTGGACTGGGTCTTCCCACATCAATGAACACAGTCAAGGCAATCCTCTACAGACATAGTCACACAGGTCAACCTCATGTATACAGTTCCTCCCAGGTGATTCTAGATTGAATCAACTTGGCAGTTTAAAGTAACCACCTATTGCTCCCACACACAACTAGCCCACTCTCAGAGGATTACTGCAAACATCTGTTTGCTTCACTAAGTAGCTATTTCTAAACATGAGCACACTAACTTTTAAAAGTATATATTTGGACTGGAGGGATGACTCAGCAATTAGGAGCACTGACTGGTTTTTCAAAGGACCAGAGCTCAGTTCCCAGGATTCATAGTAGGTGGCTCACAAGAGCTCCATGGGGACCTGGCGCCATCTTCTGGCCTTTTCAGGCACCCACATGCACAGTACAAACAATGTTACACGCATTGATACATAATTAAAATAGTCAAAAGTATGAGTGAAATTTTATCATAAATTATTTTCCTTTCCTTTCTCCTTTTATGACTGTTGGAAATATATAAATGCAGTCATCCTTTGATATCCACAAAGGAGTGGGTCCAATGTCCACTAGAATACTTAAACCCCATGGATGCTCAAATCCTTTTTTACAAAATGTTGCGTTTGAACTAACCTGCCGCCATACTCTACATTCTTTAAATCATCTTATTATCCACAGTGCAGAATACACTATATATGATGTGTAAATGGCTGCTATAGAATGTATTTCGAGAATAATGGGAGGAGTCTTCATGTTTAACACAAGTACAATTTTTTCTTTTAATCTGTAACTGCTTAAATTCACACATGTGAAGCCCACAGCCTGAATTTGAGCATTTGGGGCGCTGAGAGTTGAAGTGACGCAAGAAGAAGTTAATGAGGGTGTGTCATGGGGAAAGAAACAGCCACACTAGTGTCTCTGGGAAGGACAGGAATAGGAGACAGACCTACTGAGGGAGAAACCATCTCCCTCCTGCCCGCTAAGCCACAGATCCCAGAACACTCCAGAGAAACACTTTTCAGTCCCTAATCTTTCTAGGGAGCTGCCTGCTTATCATTCTCTGTACAGCCTGCCCCCAAGAACATGTCTGATATTGGACAGGAGGGCTAGGGACCCTGAAGGTTTGGAGGTGGTGTGGTTACCTGGGTCACAGGAAGGACACACTGCCTAACAGGAGGGTCCTGACCCCCTTTCTTCTGTGCTTGGTCTCCAAG
Seq C2 exon
TACACCCCCCTTAACCTCACAGCGCTGGACTGGTCCCTGCTGAGCAAGAAGGAGTGCCTGAGCTACGGCGGGCGCCTGCTCGGGAGCTCCTGCCAGTTCGTCCCAGACCTGGCGCTCATGTCCTTCATCCTTTTCTTTGGGACTTACTCCATGACCTTGACTCTGAAGAAATTCAAGTTCAGCCGCTATTTTCCCACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000068323-Slc4a5:NM_001166067:14
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=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0095516=HCO3_cotransp=FE(3.6=100)

							
A:
NA

							
C2:
PF0095516=HCO3_cotransp=FE(12.7=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000109533f5362A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000041007, ENSMUSP00000109532, ENSMUSP00000109533
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:74239536-74241993 
ALTERNATIVE
HsaINT0153448
(SLC4A5)
Human
(hg19)
chr2:74466663-74469120 
ALTERNATIVE
HsaINT0153448
(SLC4A5)
Rat
(rn6)
chr4:114973941-114976266 
LOW PSI
RnoINT0138522
(Slc4a5)
Cow
(bosTau6)
chr11:10382021-10382871 
LOW PSI
BtaINT0136119
(SLC4A5)
Chicken
(galGal4)
chr22:2844991-2845279 
LOW PSI
GgaINT1025723
(SLC4A5)
Chicken
(galGal3)
chr22_random:21523-21809 
LOW PSI
GgaINT0000193
(SLC4A5)
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"