Special

MmuINT0147193 @ mm9

Intron Retention

Gene
ENSMUSG00000060961 | Slc4a4
Description
solute carrier family 4 (anion exchanger), member 4 [Source:MGI Symbol;Acc:MGI:1927555]
Coordinates
chr5:89652221-89654998:+
Coord C1 exon
chr5:89652221-89652289
Coord A exon
chr5:89652290-89654824
Coord C2 exon
chr5:89654825-89654998
Length
2535 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
TTCTCCCCCATTTCTCCCAGTTC
3' ss Score
7.78
Exon sequences
Seq C1 exon
TTTATCCCGATGCCTGTGCTGTATGGTGTGTTCCTGTATATGGGGGTGGCCTCACTTAACGGTGTGCAG
Seq A exon
GTAAGCTTCCTCAGCAGTCCGAGCAAACCCTGTGCGTTTCTCAAAGCAGAACTAGTCCAGTCACCGATCTCTGATGAAGGCACTAATCATTAACTAGGGACTCTTTTAAAATACATTTATTTTCTACTTCCTCCACCTTTTACCTGCTTCTCATTTCTGATGGAATCGACAAAGCTAGCTGGTGTCAACAAATGTTATCCTGAATGCCCATTACTGAAAAGGGTTGCTAAATGTCATTTGGTGAGGAAATGAGCTGCTGTTCTCATTACCACCACCACCACCTCCTCCTCCTCCCCCTCCCCCTGCCCCCCCTCCTCCTCCTGCTGCTCGTCCCAGTCCTTCTCCTCTTTACCTCTTCCTCCCCATGCCCTTTTTCACACTCCTGCTCTTCCTTTTTGTCTTGAATTCTTTTCTCATCTCTCTCTTACATCACCTTATTTCATCTCAAGATAGATACTCACTGTGTTCTTAAGGCGGTGTTTGCGCACTTGCCTGACCCCTTATAGACAGCTTGCGATCCTTTAAAACTCAGTGATGAAAAGTTTTGTAGCAATAAGCAATTAAAATTACCATGTAGTAGTTACTGCTTTCATCAACACTTTCAGATGTTCACAACTTCAGTTAAAATGACCACCCTGCCCCCATCCCGCCTCTGCCCCCGCCCCCGCCCCCAGCCCCACCTCCACCATGCTCTACTTTTTAAAAAAATTTACTAGGAAAAACTTTGTGAGGGACTTTGTCTCTCAATGGAGGTTTAATTTAATTGGCACCAGGAAACTGGAAGTTCCGCCACTTTCTGGCACCCTGTTAATTGCAGCCTTATTTAGCACTCAGTAATGTTTTAATGGGAAAAGACTGCGTGTTCTGTGATCATCATAAGAATTCATTTGAACTCCTTCAAAACAGCCCTTGCTTTCATTTATTACATTTATATTAACTTGGTTTTAAAGTCAGATAGATCTGGGCAAATGGCCAGACCCCCCAAAAGCAAAGCTAAGCTACTTTACTATTCCTGGGTTTGGTCCAGTAGAAGGGTTCTTCCACACCGGAATATTTGTTATGAAACACAAAGTGCTTCTTCATGGGCTGCGTGGGTGACTGAGGGTTTTTTCAGTTTGTTTTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTTGTTTGCTGTTGTTGTTGTTTGGTTTGGTTTGGTTTGCCATCCAAGTAATTTAGGAAGTACAACTTTGTAAAATATTTTATTTTTCCCTGCCGTTTATGAATACTTATTCTCCCAGATGGGAAAATATGAGCATTAGATGCCTAGGACTAACAGTTATTAATTTTTGTTTGCCCTTAAGGATCCAGTCAAAAACCAGAGGTTTGTGTTGGGTGTCCCAGGGACCTGATCAATGTCTAGAGGTGAATACCTGTCTATAAAGAGAACAAAAGAGCCAATCACCCCATAATAATTGTAGGGACAGCTAATGAACTGTGTTGCTCCTTAAGTATTATTGTCCCAAACACCTTTTCAATTTTTTTTATTTTTCTCTTCATTCTTTCTCTTTTAGACCCTTTTGACAAGATTGGTTTAGCAAGGAAAAAAAAAAAAAAGAAATCTAATCTTTATAGATAAGAATATATTCTAAAGGGAGAACAAAAACTATCATATAGGCAGAGGCTCCAGAGAAGGTTATGATAAAGTCGCTTACTTTTCCTTAATTCTTATAATTAGTCAGCTCAGCATCTGTCTATGCAGCGTCTCCCTCTGAAGGCCCCTGGATGAGGTACTGAGCATCATTGTACTCTCCTCATAGTGTCACCTAAGTACTACATCTCTGGGATGCTCCTGGCACAAATATCCACCATCATCCTTCCAATTCCTGACCAAAACATGACTGTGTTAACCACTCTCAGACTCTTGAGTCTTGTGGTCGTTGTCTTAAAACTCACCATAATGCTCACAGAGCTTTTCTCTGGAAGAAATGCTGATACACTAGTGGGTATGGATGTGTTAATAAATTATAACCTAAAGAAAGTGGGACTTACTGGCATAATCCGCATGGTTCCATTTTTAAGTTAGATGGGTCCTTTATCTCCTTAGAGCATGACTGATATGCCGATGTTGTGGTTTTTCTTTCAGATAAGACAACTGAGGCAGGAGTAGATGCAAGAGCTAGGAGTCTTCCCTCAGCATAGTGTACCAAAATGGGTACACAATCCTCTGTGCTGAAAAGCAGAGAGTAGAAAGAGAAGGCAGAGGATGAGCAGCTAGAATTTAAGATTTCCTTATAACTTTAGCCTTTGATGCCCACTTTATCTTATGTACCCGCTAAATATCTCTGGGGAAAAAAATCAGCAGAAATTAGAAGACACGTAACATAATATGATGTGACTGGGCTAATGTAAATCCCCCACTCTCTAACCCAAGCTTTGTCCTTTGAAGAGGACATTGTTCGCCTGAAATATACACTATAAATCACTCCTGGCTGGCTAAGCAGAGAGGAAACAACTCAACAGACTCTTCAGATAACACATCGACTTTTTCTCCCCCATTTCTCCCAG
Seq C2 exon
TTCATGGACCGTCTCAAGCTGCTGCTGATGCCCTTGAAGCATCAGCCCGACTTCATCTACCTGCGCCACGTCCCCCTCCGCCGAGTCCACCTGTTCACCTTCCTGCAGGTGTTGTGCCTGGCTCTGCTCTGGATCCTCAAGTCAACAGTGGCTGCAATTATTTTTCCTGTTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000060961-Slc4a4:NM_018760:21
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(4.2=100)

							
A:
NA

							
C2:
PF0095516=HCO3_cotransp=PD(6.5=58.6),PF103594=Fmp27_WPPW=PU(0.1=0.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000121744f5179A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000108844, ENSMUSP00000118413, ENSMUSP00000119325, ENSMUSP00000121744
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr4:71555209-71557711 
LOW PSI
HsaINT0153430
(SLC4A4)
Human
(hg19)
chr4:72420926-72423428 
LOW PSI
HsaINT0153430
(SLC4A4)
Rat
(rn6)
chr14:20491532-20494044 
LOW PSI
RnoINT0138504
(Slc4a4)
Cow
(bosTau6)
chr6:88528200-88531379 
LOW PSI
BtaINT0136101
(SLC4A4)
Chicken
(galGal4)
chr4:49775996-49777683 
ALTERNATIVE
GgaINT0077111
(SLC4A4)
Chicken
(galGal3)
chr4:51862587-51864274 
ALTERNATIVE
GgaINT0077111
(SLC4A4)
Zebrafish
(danRer10)
chr5:45157593-45162543 
LOW PSI
DreINT0151532
(slc4a4a)
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"