Special

MmuINT0147271 @ mm9

Intron Retention

Gene
ENSMUSG00000023032 | Slc4a8
Description
solute carrier family 4 (anion exchanger), member 8 [Source:MGI Symbol;Acc:MGI:1928745]
Coordinates
chr15:100615146-100617783:+
Coord C1 exon
chr15:100615146-100615306
Coord A exon
chr15:100615307-100617594
Coord C2 exon
chr15:100617595-100617783
Length
2288 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
TGGTTGGACTCTGCTTTTAGACC
3' ss Score
5.75
Exon sequences
Seq C1 exon
GTGGCTGAAGTTTGAAGAGGATGTGGAGGACGGGGGAGAGCGCTGGAGCAAGCCTTACGTGGCCACGCTCTCTCTGCACAGCCTGTTTGAGCTGAGGAGCTGCCTCATCAACGGCTCTGTGCTTCTGGACATGCGTGCAAGTAGCATAGAGGAGATCTCAG
Seq A exon
GTATGGGGCAAACGATGGGCAGAGGAGTTGGGCGTAAACTCGGAAGTATGAGAGCCAAGCATTCTGGCTCACACCCGTAACCTGTCATTAGGAGGCTGGAGAGCAGAATGCCAGCTTTGAGGTCTGAACTCTACAGTGATACTTTATCTCAAGCAAAACAAAACAGAACGTTGAAGCCAGAAAGGAAGAAAGTTAAAGGGTCATTGAGGCGGTGTTTGCCGTGCCAGCTGGGCAGGCGGCCTTAGTGCCATCCCAGGAATCGGTGATGGAAGGACCAACTTCCGGAAGCCGTGCTCTGACCTCCACGAGCTCACCATGGCACTTCCTTTCATCACATACACGCGCACACACGCACACAGTAGTGGTGGTGATAGTAATAATACCTTTTAAAAAGTAAAGATTTAAAAGCACACACTCTTCCTCTAGAAGAGATACAGGAGGTGAGCCATGGCATCCCACACTTCAGCATGGGGTGCGGGGTGGCCAGTCTGGTGTGAGCAGATGTTAAGTTACCATGTTTGGGGAGCAGCATTGGAAAGCACAAGTGTCTAGGTGATTCTGCCTCTCTGAGGAGGGGGACCTGGGGACCGAGGCCAGTCCTGATGGAATCCTGTGTCGACTCCTTTGAAAGGTGGTGCCTGGGTGTGCCACCCACTGTGGGGAAAGTGGGATTAAAAAAAAAGTTCTCTGTCAGTGCCCTGTTCACGGCTGCCGAGGCAGCGGAACCTGGGGGGATTGGAGGCCATAAATGAGCATCAGAGAGGCCATACAGTTTGTATGATGCTGAGGGTTAAAGGGCGTCACACGAGTAAAGTGTGTCTCGCCAAGTCTGAGCTGCACGTGGCGCCAGCTAAGCCTTTGCACCGGGCAGGCAAGCCGCACGTAGCAAAAATCGTTTTTTGTTTTTTTGGGGGGTTTTTTGTGGAGGCTTATAAACAAATAGCAATAGCCAGGTATAATCGAAGTGAACTCAGTGCTGTCCACTACACCTGGCAGGGCGTGGAAGCACATCCCCACACTGCGTTTGAAGAAACTGAGGTCACAGGACATGGTTTTTTGGAGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCATAAGCACTCAGAAGTCTCCTCACACTGCTCCATCCTTGAACTGTGTTCCAAAAGGGTCACAACTGTCTTTCACTGACTTGTAACTACATACGTGTCTAAGAGCCTGCGAAGTTCCTAAGAAAGTGTGTGCCGTGTTTTGGATAGAGGAATCCCTGGGAATTAGTGCCCTACAGCCCTCAACAATGAGACCTCAGCCAAGCCTTGGCAGGGCAGCTGTAAGAATGATGGAGGCTGAGTTAATACGTCAGGCCATGGGAAGAGAGGAGGCAGAGCGCTGCCTGCATGGGGCAGTGGCGGAAGGGCACTGTTTCCAATGCAGCTCGGGAGGTAGAATTGATGGTAACAACCTGGTGGCATCCAGATGGCAGTGTCTGTGTGTAATTGGAGCTGCCATGACACTTGAGAGACAGATCTGAACTGAAATGTGCCCCTAGGTCTTCTAAAGGTGGTTCAGGTTATTGTGGTCAGCAGTGGGGGTGGGGACTCCACCTGTCTGAAGCTGGCTCAGGGGTCATAGGTTGGGTGAAAGAAAAGTATCACCCTTGGAGACTGAGGGCCACTCAGCAGTGTCACAAAAATCGGACAACAGCCACCAAACCTGTGTTACCCTCCTAGGACTGCTGGGATACATCTCCATCCGTGTGGTGGCTCGTGCCCGTGATCCCAGCATCCAGAGGTTAAGGCAGGTAGATGAGGTTCAACACTAGCCTGGGCTTGTAGCAAAGTCTTGTCTCAAAATAAAACCAGTGAACCAATCAGTAAGTTTGGAAGTCAGAAATCTGAAATGAGTTTAGTTTGGGCTGCATTCCTCAAAGGCCCACAACAGGAACGTTTCTCCAGCTTCCAGCTTCCGGGAGCTACAGGTGCTTTTTTGTTTTTTGTTTTTTGAGACAGCGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAATTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCATGTGCCACCACGCCCGGCTACAGGTCCTTTTTGATTGAGGATTTTCTTTTCTTTTGGGGAATTTTAAGAGGGAAAGGAAAAATAAAACTAGTAGTAGAGGGTGGAGCAGCTTGCCGCCACCCGCTGCTCCTTCCCCGAGCACCTGATGCGGGTCCTCTGTTCCTGAGTGTTGGTTGGACTCTGCTTTTAG
Seq C2 exon
ACCTGATCCTGGACCAGCAGGAGCTGCTCCGAGACCTGAGCGACAGCGTGAGGGTTAAAGTGCGGGAAGCCCTGCTGAAGAAGCACCACCACCAGAACGAGAGGAGGAGGAACAACCTCATCCCCATCGTCCGCTCCTTCGCTGAGGTTGGCAAGAAGCAGTCTGACCCGCACTCCATGGACAGAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023032-Slc4a8:NM_021530:5
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=0.250
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF075658=Band_3_cyto=PU(18.2=85.5)

							
A:
NA

							
C2:
PF075658=Band_3_cyto=FE(24.4=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000023776





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000023776f1399A, ENSMUSP00000023776f1400A, ENSMUSP00000023776f1401A, ENSMUSP00000125090
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:51453700-51457350 
ALTERNATIVE
HsaINT0153515
(SLC4A8)
Human
(hg19)
chr12:51847484-51851134 
ALTERNATIVE
HsaINT0153515
(SLC4A8)
Rat
(rn6)
chr7:142428476-142432713 
LOW PSI
RnoINT0138585
(Slc4a8)
Cow
(bosTau6)
chr5:28511628-28514177 
ALTERNATIVE
BtaINT0136185
(SLC4A8)
Chicken
(galGal4)
chrLGE22C19W28_E50C23:865311-866196 
LOW PSI
GgaINT1025754
(SLC4A8)
Chicken
(galGal3)
chrE22C19W28_E50C23:851139-852024 
LOW PSI
GgaINT0000820
([1])
Zebrafish
(danRer10)
chr6:40380471-40383675 
LOW PSI
DreINT0151612
(slc4a8)
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"