Special

MmuINT0147205 @ mm9

Intron Retention

Gene
ENSMUSG00000068323 | Slc4a5
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 5 [Source:MGI Symbol;Acc:MGI:2443220]
Coordinates
chr6:83218188-83221091:+
Coord C1 exon
chr6:83218188-83218376
Coord A exon
chr6:83218377-83220916
Coord C2 exon
chr6:83220917-83221091
Length
2540 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCCC
5' ss Score
5.96
3' ss Seq
CTTCTGCCTGTCTCAAGCAGGTT
3' ss Score
7.26
Exon sequences
Seq C1 exon
GAAATCTGTGTTCTCTCTGGCAGAGCCGGGCCAGATGAATGGCTCTGTGGGCGGAGGCGGAGCCTCGGCTGGAGGAGGCGGCAGTGGCGGAGGGGCTGGAGGCAGCGGGGCTGGCGGAGTGGGCAGTGGCGACGAAGCTGAGATGCCAGCTATGCACGAAATCGGGGAGGAGCTGATCTGGACCGGAAG
Seq A exon
GTGCCCGCTCCACACCTGGCAGAGAGCCTGCTGTCCTGAACCCTTCCTTCTTCCGGTCCTGTTAGCGATCCTCTCGCTGCTGTGTGCAGCGCCCCTTAGGGACGGGGATCTGACCACTGCAGTCGTCCCGCACTCTAGTGAATCGTGTGGCTCTGACAGAATTGTGTGGGGTGAGATGAACAGAAGGATCCCACCCGTGAGGAAGGAACCGAAACATTTCTCTAGGCATTCTTTAGTAATTGTATCCTATAGCGGCAGAAACAACGTATCACAAGCAAGGTAGTGTAAAATTACTGACGTCCATTTTCACATGAGTGTGAGATCAGAAGGTTAAAATGGAGATGTCACCAGGGAGCAGAGCCTTTGTGGATCCTACCTCTAATTCCTGGCACTGGAAAGACTGAGGCAGGAGGATTGTTGCAAGTTCCAGGCCAGCCTGTGTTATATAGTGTGAGGCCCTATCTCAACCCTACTCCTTAAATAAAGATGCCAGCAGTGCACCACTGCCTTTGAGCCTCTAGGAACGTCCTTCCTCTCCTTGAAAGACAGCCAGGAGTCTCATAGCACTCCTTGATTTGGCTGTTGTGTCACCTCAGTTTTTGTGTATAAATTTCCATGGCCTTGTCCCTGTGTGATATCTTTGGATAGTATTGCCTGGTTTCTATAATGGCTGGATCAAAGCATTCTTAATGAGTTCATTGTAACTTAATTACATCCTCTCTGCCTCCCTCTCCCGCCCCTTTGTGGTCTCAAGTAACCCAGGTTGACTTCAAGCTTGCTATAGCTAAGGATGATTTTAAATTGATGGTGCCCCCGCCCCTTCCTCTCCAGTGCTGAATTCACAGGCACCACCATGCTTGTCTTATAAACCAGGGCTTCATGCCTACCAGGCAAACATTACCAACTGAGCTTCATTCTCAACCCAGAGACTTTCTAAGTAAAACCATATTCACAAGTATACCAGAGGTTGGAGATTTAATGTATCTTTTAAAAAGAAGCAAGATCTTGAAATCTTAATTTTTTTTTTAAAGCTTCATTTTTCTTTCTTCTGGGGAACAAGAAAAAACTTTCCTGGCCTGAGTTCCCTGGCTGCTCTTGGAGTCACCTAGGTTGACCTAGGTTTAGGGAAGTCCAGAGAAGTACAAGGCTCTGTGCAACCGAAGCCGTTGGGAATGAAGCTGTGTGCTGAGTCTTTCTCGCTGTGATAAGATTCTCTGACAAAAGCAACTGAAGGGAGAAAGGTTCGAAGTTTAAGTAACAGCAGCTCATGCTGGGAAAGTCAAAGTGCAGGAGTTGGAGGGAACTGGTTACATTGTATCCACAGATACATTGTATCAAGACACGAGAGCATTAAGCTCTGGCTCATTTTTTTCCCCAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTTCGAGGCAGGGTTTCTCTGTGTAGCCCTCCTGTCCTGGAACTCACTCTGTAGACCAGACTGCCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGAGATCAAAGATGTGTGCCACCACTGCCTTCTTTTTCCAATTTTTATTAGGTATTTTCTTCATTTACATTTCAAATGCTATCCCGAAAGTCCCCTATACCCTCCCCTCCCTCCTCTACCCACCCACTCCCACTTCTTGGCCCTGGCGGTCCCCTGTACTGAGGCATATAAAGATTGCAAGACCAAGGGGGCCTCTCTTCCCAATGATGGCGGACTAAGCCATCTTCTACATATGCATCTAGAGACACAAGTTCTGGGGGTATTGGTTAGTTCATATTGTTATTCCACCTATAGGGTTGCAGATCCCTTCAGCTCCTTGGGTACTTTCACTAGCTCCTCCATTGGGGGCCATGTGTTCCATCCTATAGCTGACTGTGAGCATCCACTTCTGTGTTTGCCAGGCACTGGCATAGCCTCACAAGTAACAGCTATATCAGGGTCCTTTCAGCAAAATCTTGCTGGCATATGCAATAGTGGCACTGGCTCATTCTTAAGCACTGGCTCGTTCTCATCTCATTGTTTCCATTTTATTCAGTCCAAGATCCCCTGCCCAGGGAGCAGCCTTACCCTCGGTCAAGATGGGTCTTCCCAATCAATCCACAAAGTCAAGATAATCCCCAACAGACATACACAGAGACCCATCTCCCAAATGACTGTAGATCCTGTGAAGTTGACAGTTCCCACTAACCATTTCATGTTACATGGCTTGGGTTGGGTAAGGACAGGAGGAAGACCCCCTCATAGTGGAGTATTCCCATCAGAACTTTCTTCTCTCAAACAGTTTGTGTCCACCTTCCCCAGTATGGATGGTGATGACTGCAAATTTCTAGGCCTACAAGAATCATGTTTGGCTCTCAGTGTTCTGGTAGAAAGAGTGTGACTCCATCTATCCCTGATCCCTACTCCAGACTCTTGAGGGCCCTGGAGGCATCCCCATCCCTCCTGGTGTCTGTGGAGGAAAGATGTCTTCTGCCTGTCTCAAGCAG
Seq C2 exon
GTTCTTTGGAGGACTGTGTCTGGATGTCAAGAGGAAGCTGCCCTGGTTCCCAAGCGACTTCTATGATGGCTTCCACCTCCAGTCCATCTCTGCTGTTCTGTTCATCTACCTCGGCTGTATTACCAACGCGATCACCTTTGGTGGGCTTCTGGGGGATGCCACAGACAACTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000068323-Slc4a5:NM_001166067:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.547 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0095516=HCO3_cotransp=PU(1.2=9.4)

							
A:
NA

							
C2:
PF0095516=HCO3_cotransp=FE(11.1=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)
chr2:74250518-74252178 
ALTERNATIVE
HsaINT0153444
(SLC4A5)
Human
(hg19)
chr2:74477645-74479305 
ALTERNATIVE
HsaINT0153444
(SLC4A5)
Rat
(rn6)
chr4:114965249-114967355 
ALTERNATIVE
RnoINT0138518
(Slc4a5)
Cow
(bosTau6)
chr11:10372288-10373945 
LOW PSI
BtaINT0136115
(SLC4A5)
Chicken
(galGal4)
chr22:2849277-2849443 
ALTERNATIVE
GgaINT1025719
(SLC4A5)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr5:27474380-27476840 
LOW PSI
DreINT0019530
(SLC4A5 (1 of 2))
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"