Special

MmuINT0146272 @ mm9

Intron Retention

Gene
ENSMUSG00000029188 | Slc34a2
Description
solute carrier family 34 (sodium phosphate), member 2 [Source:MGI Symbol;Acc:MGI:1342284]
Coordinates
chr5:53459583-53462902:+
Coord C1 exon
chr5:53459583-53459707
Coord A exon
chr5:53459708-53460233
Coord C2 exon
chr5:53460234-53462902
Length
526 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGC
5' ss Score
7.16
3' ss Seq
CTTCCCACCCTCTGTTTCAGATT
3' ss Score
11.2
Exon sequences
Seq C1 exon
GTATTGGGGTGATCAGCATTGAGAGGGCATATCCACTCACGTTGGGCTCCAACATTGGCACCACCACCACCGCCATTCTGGCTGCTTTAGCCAGCCCAGGCAACACCTTGAGGAGTTCTCTCCAG
Seq A exon
GTCAGCAACTGCTACCGGGCTCTGGGTGGGATAGAACCTGTCTGTGCTTTGGTTTTGGTTTAAGTCAGAATTTCATAAAACCCATGCTGGCCCCAAATTCATAAGGAACGGCCTTGAGAGGTCCTGCCTCCTCTGTGCTGGGAATGGATGCACGCCACGGCCATACCTGGTATATAGACTATTTTCTAGTGAGAGCCATGCACTCTCTTCTATCCATAAGCTACTGGGAGAAACCACATGGAGCTATGTATGAGGACAGTCAAACCTATGGGTTCCTAAGAGGTGGGCGTGTAAAACATCTACGCTGCTGAGACAATAGGCCCAGGTATGGTGAAGCAGCAGGCAAACCCGTATCAGATGACACCTTCCGGACCTGAAAGCTGAGCTCTTCAGTGGGGTTACTTCCTTCTTCCCCTGATCTCCAGACAGTAAAGTGATGGGTGTTCACAGAATATAATGCTCTGCACAAGCTCAACTATACACAAGACCTGGAGTGACTCTTACTTCTTCCCACCCTCTGTTTCAG
Seq C2 exon
ATTGCCCTGTGCCATTTCTTCTTCAACATCTCTGGAATATTGCTTTGGTACCCAATCCCATTCACCCGTCTGCCCATCCGTCTGGCTAAAGGCCTAGGCAACATCTCTGCCAAGTATCGCTGGTTCGCAGTCTTCTATCTCATCTTCTTCTTCTTTGTGACCCCGCTGACAGTGTTTGGCCTGTCTCTGGCAGGCTGGCCAGTGCTGGTGGGCGTGGGCGTACCCATCATCCTGCTGCTGCTCCTGGTTCTGTGCCTCCGGATGCTGCAGTTCCGCTGCCCTCGCATCTTGCCCCTGAAGCTCCGGGACTGGAATTTCCTACCCTTGTGGATGCACTCTCTGAAACCCTGGGACAACGTCATCTCCCTGGCCACCACCTGCTTCCAGAGGCGTTGCTGCTGCTGTTGCCGCGTGTGCTGCCGTGTCTGCTGCATGGTGTGCGGCTGCAAGTGCTGTCGCTGCAGCAAGTGCTGCAGGGACCAGGGAGAGGAAGAGGAGGAGAAGGAGCAGGATATCCCGGTCAAGGCTTCTGGGGCCTTTGACAATGCAGCTATGAGCAAAGAGTGCCAAGATGAGGGCAAGGGCCAAGTGGAAGTTCTGAGCATGAAGGCCCTGTCCAACACTACAGTGTTCTAGGGGCACCTAGGAGTCAGGGGTGAGGAGGACCTCAGGTCCCATGGGATCCACCCCTTCCGTAAGCGTCTCCAGCTACCTCGCTAGGATTTCTGATGAGGAAGAATAACACCAACTCTAGCTCTCCTACCACCAGAGTAACAGTCTGTAGTTGAATTGGACTTATCTTCTCTGCTTCTCAAGTGCCTCCCTCTTAGAAGACAATACAGAGAGGCCTCAGATGACTTCATCCACCTCTGGCTTTCAAAGCCAATCCTCACCCAAAGGTCAAGTCTTAAGGGAGGCATTAGGGAAGGTTCTGGAAAGACCCAATGTAAAGAGTATTTGTAAATATATGTACAAAGCAGTCATTTCTTGGTATGAAACCTCAGCCACATCTTTTTTTTTTTTTATCAAAGTCTACTCCCCCTACTCAATAGCTCCTCCTCCTATTCGTCCCTGCCCCAGAGCAGCCAAGTCCAAACAGTGAAGTAATGGCTTGGAGCCCATAGATGTAAGCCTCCATAGCTTACATTGCAGGAGATGTTCTCTATGGAGGAGGCTTCATCTGGGTATAGTCAGATCAAGCAGTTGACCCCAGTGTCCTCAGCTTCAGCTTCCTAGGATGGAGAGACACATGGTTGGGGTTCATATTTGGTTTCTGTACGTAGGGCTCTGGATTAATCTAGAATAGGAGGCATTGGTGTTCTTGGTCAGAGTAATATTGCTGATGGAACCTGTAAGACCTGTGTCCCAAGCCCTCTCCGTTGCTACCACTCGGGACCATCTGCTTGTGAAGGGTCTGTTTATCTTGTTTTGTGCAAGGAGACTTGCTGGGCCAGCCTTTAGTGGTCTGTTTCCATCCACCCACTCACCCTCTTGCTCATGAAACATGTTCCCATCTTCCATAGGTGAGCTTTGTCCTGCCCCTTTCCATGCCTACAAAGCTCCAAGGGAATTCTTAGGAGGGAGGAGATAGGAAATGGCTAGATGCTCTTAAGAGTCAAGATGAAGCCAGTAGGGTTTGGAGTGACTGCAGGTAAAGGGTGGGATCCTATTCATACAGGATACCTGTGCCTTTTAGAGCCCACGTGTAATACCCACAATGGCTCTGCAACCATCCCCATAACTCCCCCCACCTCCCATAAGAACAAGCCTCAGCTTGACTTAGGGCAGGTGTGGCTCCATAGGACCATGTCCTCTCCATCCTCTCCCATCATGCTCTTCGCCATAGGAAGAGGTGGAGATGCCAAACTGAGCCCCTCTGTAGATAAAAGTTCCCAAAGAGCCATTTATGTGGCATATTTATAGCTATGCATCTGTACAGAATACTTCATAACTTATACATAGTAAATAGTGATTTGTTTTATAGTGTCTCATTTGGAAATGAGGCAGGGTTCTTTTATGTACTGTGAAAAGAGCACCTTTGTATATTTTGTAATACTGCCTTTAAACACAACTCTCTGAGGCCACGCTATACCTCCCTGTAAATATGTAAGTTACACCCCAGGAGGTGGCTTTGCCCTCTGTTGATTATATATATTTTTTCTTTTTAAAAAAATGGGATCCTTGTTCCCATGTTAATTGTATTTTTTTAAACTGGTTGAGGAAAGGGGGAAATAAAAATCACACCCCAAGCCCCCCGCCCCCCGCAAGTGTGCTGCTTCCAATTGCAGGGTGACAGGAGGTATCTTTCCCTACTCAAACCTCACCATGCATCACCACGGGAAGCTATGTAGTTTCTGGTGACACTTTGGGACACAGAGGACTTAGTCCCACCTTCAGTTTTCTCTTTTCCAAGTCATGGGGATAAGCTACTGAGAGCTATGCTAAGCAAAGCATAACATTTTGTAGTTAATGAATGTTACCAGGTTTGGAAGCAAAGACTCGGGTGGAATCTTTGAAATCACACAGTTGATGTTTTGAAACTATGTGCAGGCCATCTTCTGTCTTGTTTTTAAAATTTCTACATTAGAGGGGGAAGGGGGCAGTGAGTGGGATGTAAATTGAATAAGTAAAAATTTAAAAATAAAAACAAATTAATTCCAGTACTGTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029188-Slc34a2:NM_011402:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.005
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0269010=Na_Pi_cotrans=FE(29.3=100)

							
A:
NA

							
C2:
PF0269010=Na_Pi_cotrans=PD(22.1=14.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000092380





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000132328
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr4:25674630-25676134 
LOW PSI
HsaINT0152511
(SLC34A2)
Human
(hg19)
chr4:25676252-25677756 
LOW PSI
HsaINT0152511
(SLC34A2)
Rat
(rn6)
chr14:60259214-60259753 
LOW PSI
RnoINT0137612
(Slc34a2)
Cow
(bosTau6)
chr6:46747269-46749070 
ALTERNATIVE
BtaINT0135292
(SLC34A2)
Chicken
(galGal4)
chr4:73039142-73039893 
ALTERNATIVE
GgaINT0072516
(SLC34A2)
Chicken
(galGal3)
chr4:75885330-75886081 
LOW PSI
GgaINT0072516
(Q6TQF9_CHICK)
Zebrafish
(danRer10)
chr23:1089972-1093482 
ALTERNATIVE
DreINT0150671
(slc34a2b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GGTGATCAGCATTGAGAGGGC

				
R: 
CAGCAGCAGGATGATGGGTAC

				
Band lengths: 
358-884

			

		

	





	
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"