Special

MmuINT0147242 @ mm9

Intron Retention

Gene
ENSMUSG00000021733 | Slc4a7
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 7 [Source:MGI Symbol;Acc:MGI:2443878]
Coordinates
chr14:15618806-15623678:+
Coord C1 exon
chr14:15618806-15618937
Coord A exon
chr14:15618938-15623580
Coord C2 exon
chr14:15623581-15623678
Length
4643 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAA
5' ss Score
7.3
3' ss Seq
TTCAGGTCTGTTCTTTCCAGGAA
3' ss Score
8.43
Exon sequences
Seq C1 exon
GTTCTTGCATTAGTCTTTGTGCGCAAGCTCATGGATCTCTGTTTCACAAAGAGAGAACTCAGTTGGCTTGATGACCTCATGCCAGAAAGTAAGAAAAAGAAAGAAGATGACAAAAAGAAAAAAGAGAAAGAG
Seq A exon
GTAAAAAGGCATCCCTTCGTTCAAGGATTTGTACCATTTAGCAGATCCTCAAGGAAGCTTAATGAAACACAAGCCATGCTGAGTATTCCATTTTACTGAATGCGGCAGAGGGGGTAGGCAGGGTTACCCAAGCACTGCTTCTTACCCATTTCCCCACCTTGCATAGTCTGTAAAACTAAAAACAACAAAAACAAACAAAAATAAGGTTTAGCAGTATTAAAACATCACACAATAATTTTATGACTGATTTAACCTTAAATACCATAGGTATGTTACTGTGTAGTACAGTAGCAGTACTTTAGTGGTCTGACATACACTAATGGAGTGTAAATGTGTTTAAGAGTCTTCATCTGATAAAAGCATTTACTGTACAAGCACGGGACCTGAGTTTACAGTCCTTACCTGCACCCAGTTTAAAAGCAGGGAGTAGTTGTTTGTACCTGCAACTGCCGCCCTCTGGATCCTGGACAGGAAGCATAGCTCCAGAGTCAGGAAGATACAACTGTATCAAAGCAGTAGATGGAGTCTGATTGTCTTAGTTTGGATTTTATTGCTGTGAAGAGACACCATGACCAAGGCAACTCCTATAAAGGAAAATATTTAATTGAAGAGGCTCAATTCATTATCATCATGGTGGCAAGCACAGCATCCTGCAGGCAGACATGGTGGTGGAGGAGCTCAGAGTTCTGCATTTTGATCCAAAGGCAATCAGAAGAAACTAGATTCCACAGGCATCCAGGAGGAGGCTCTCTTCCACACTGGGTGGAGCTTGAAAGCCTATTTCCACAGTAATATACTTCCTCCAACAAGGCCACACCTCCTTTCCATATGCCAAGCGTATTTAAACCACCACAGTTATGGAACAAGACACCCATAATTAAGCATGCATCCCTCAAACTATTGTATGTTTTGGGACAGAGGTTTTTGTCTATCCTGCTGTTGAATTCTTGGGCACAAGGATTCTTTCCCCAGCTTTCCAAGTAGCCGGAAGTAAGGCATACTGCCGCAGACCCTCTGGGTCCCTGGTCTGCGTGGAACAGGATCTCTTAAGCAGATGGGCAAAGAGTCGGATGGGGTGACAAACAGACGAACACACAAGAGTGGTGTTGGATCTGAATGTAATTTTCCAGTCGAGCCTCAGACTTTTATAATACAGAGTAAATTGCAAATCATAACAGAATAAGGCACATTGAATTTTTCCAGGTGCAAAAGGAGTGACTACAAAAGGAACCAGATAAATGTTTAACACTAGAGATTAGCACAGATGCAAGGGGAGTGACTTCAAAGGGAATTTGTACAGACCAGATAAATGTTTACAGTAGAGATTAGCACCTTCTGCCAGGTAAGAGTTTTACACTTAGTGTTAATAGCACCAGGGTTATTAACTCTTGACACGCCTCAAGAATAATGTAGTGTCAATGACCCCAAAATTCTCTAGGCCTTGTTAAATTATCTTGTCTGAAGGATCCTCATTTATCAGTATAGTATATTAATTTGTTCTTGGCATGGAATGTAGTCTGTAATACGAATTTCTATCTCAGTGAGAATTTCAGACTCTTTCTGCAGACAACTGAATTAATGGCTAGTGCTTTATTGTTTTATGGTAGTGCTTAATTAGTTACTGAATGAGTTAAGCTCCTTGCTGCTATCTGGAATCTAAGAACACTGGGAAAAGGCTTTAGCTATGTTAGAATTCAATCTTAATGGCCTAGTCGGCCATCACTGGAAAGAGAGACCCATTGGACACACAAACTTTATATGCCCAGTACAGGGGAACGCCAGGGCCAAAGAAATGACAATGGGTGGGTAGGGAAGTGGGGGACTTTTGGGATAGCATTGGAAATGTCATTGAGGAAAATACGTAATAAAAAAAAAAAAAAAGAATTCAATCTTAAAAGGCATTTACTATAAGGTAATACTATATAGAGTGCACGTGGATCCATACACTAGACTAATGTGGATTTGGAAAATTAATTTTATGGGTTAGGGGAATAGCCAAAGATCCAGGAGTAAGTTTCCTTGAAACTCTTTCCTCATGAGAAAGCTTTCAGACTTTCATCTGTCAAGCTGACTCCACCGGGAGTCCCGTGGCAGCATACCACCATGCCTGACTGCTGTGTGTTAGGCTTTTGTTTTGAAATGCATTTATTTATTGTTCTGTGTTTTTGTAATGCACAGAATCTGTATGCTACAATACACATTTGGAGATAAGAGCACAGCTTTGAGAAGACAAATTTTGTAGACTTTTATGAGGATTATGGGGTCGGATCAGGTTGCCAAGCTTAAACAGCAGCAGGCTCTTTTTCATTCTGAGCCTTCTCTCTGGCCTGGATTTTGTTCTCATATTCACTATTATGTACCTCCATTCATTGGTCGATACAGTTATTTAAATATGAATACTTTATTCTGGATTTGATGTTCTGTTTTTAAAGTATTTTTATTCTATTACTAAATAGGAAGTATAAACTGCATATTGTTTTGTTGATTGTAGTATTTTCCTCAATATTATCTTAGTTAGGGTTACTATTGCTGTGATTAGACACCATGACAAAAAACATCTTGGGGAGGAAAGGGTTTATTTTATTCACAATTATTTTCAAAAGTAGTGAAGGCTGTAATTCATGTAGGACAGAAACCTGGAGTCAGGAGTTAATGCAGAGACCATGGAGGAGTGCTGTTTACTGGCTTGCTTCCCATAACTTGCTCATCTTGCTTTCCTATAGAATCCAAAACCAGTAGCCCAGAGGTTACCCCACCTGAGCCTCCCCCATCAGTCATTCATTATGAAAATGTCTTACAGACTTGCCTATAGTTGGATTTTTATGGAGGCATTTTCTCAATTGAGGCTCCTCTCTGAAGACTCTAGCTAGCTTATATCAAGTACTAACTTTTAAAATGTCATGGTGCTATTTAAATACAGATAAGAAAAAGATATACTTTTCAGCCAGAATTATAACTAGAATAGTCATTGTAACTACTTGAATGATGATCTGATTTTAAAATAAAGGAGTTTTGATTCCCTTAACACTGCATGCAAAAATATGTACATTATTGGTTATTTTTCTTGTAAGATATTGTTTATTTGCAAAATATATAAAATAAGCAGGTTATATTGCTTGGCTTTTGTATTACTTGGTTCAGAACCATATAAATTTAAAGAACAAAAATGAAAATGCATTTTAAATGCCTAGGGATCTATTTTCTCACTGCTTTTTCTTGGGGATTTTGTGTTACTGCTCCCTGTGTCAAGCATGTAGTCTCCATATCCAGATTCACCTTCTGGATCAGATTAGCTGATAAAGCCCAGCTATCATGCTAGAACAGAATCAGTAGGAAGAGCGCACAGGCAAAAATGAACATTATCTGTGTGGGGGAAACATTCTAAAACTGTCATCCAGCTTGTCCAAGTTTTTCCCCACTGAGTTACAAAGAACGCTGGGATTTTAGTGTAGCAGTTGCAAATCTGGGTACATTGTCATGTAGGCATAATGTTTTTGTCCGGTGTGTGAAGATTATCTTTGTGTTATTCAAATATTGATTTCTCTGCCCTCATATCTTGCTTCAATCTGGAAATATGTTGTAGTACTTACGTAAAGAATCTCCTGTCTCAAGTTTGTGTTAATAATTTACCATTTTATTCTCTGCCTTGTCAATCAGCCAGCAGCTGGGCAGGAGAGAAAAAGGGTTATGTCATGGGAGGGGGAGACAGAGAAGGATAAAGAAGATTAAGACATAAAGGAGGAGAAGGAACATCATGGAAAAAATGTATCGGAAGCTCAGAGAGCAAGGCCAATAGGAAAATGCAAATGTCTTGGGGGTTTGAGCTAGGAGGTAGCCACATTAGTTTAGAGGATTAAAATAGATCAATGAGTGACCAGGTATTGCAGTAAACCTTGATTACATAAGTCTTGGTCTCTTTTATGACATTTATTGGGGAACAGGCTAGGAAAAACAACTGCTATATCAGCTTACTGCATGCATTTTTATATTAAATTTACTACATTGTCACTTGGAAATGGTGGGATTTCTGATAATAGGGAGATGAGCTTGAATACTTTCTGTCCCCTATACTTCTTTGGGTCTTTCGACATTATAAATGGGTCATAATTTTAGTCCCATAATTTTGTTCAGGTGGTTTTCAACCTTGGATGATGTCCCACCAAAGGGGCATTTTCAGTGTCAGCGGTACCTCTGTATCACCACTGGAGGGATAGTGGCACACAGTTCCATTTGGACTTGAGAAATGTCTTGTATCCACAGATGTTCCCCTAAAACAAGCATGCTTTGTCAGTGTTTCTGAGGAAACTCAACCTCATAGACAAGCTTTTGCTCTACACTTGTTGAGACACGAGTTTTCAGTTTTATCTTCTTTGCTATATGTGTGGTAACTAGTACTCAGACTTAAGTCGTATTAATTTTCAGAAATAGAGGTTATTCCTTGGGAAATAAGTTTGTACAAGTAGTTATCTTAATTTCATGCTGCAAGTATGTGTTGTTTATATTGCCAGAGTTTTCAGTTAGGAAGGATACATTGTTTAAATAATGCTGTTAGTTTGGCTTTCCACATCTTTCAAGTCTTTCTGATACAGACCCTCCGGGAGGCATTTTGGAGGAAGTAATCTCTTCAGGTCTGTTCTTTCCAG
Seq C2 exon
GAAGCTGAACGGATGCTTCAGGATGATGAGGACACTGTGCACCTCCCATTCGAAAGAGGGAGTCTCCTGCAGATTCCAGTGAAAACTCTAAAATATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021733-Slc4a7:NM_001033270:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.273 A=NA C2=0.182
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000058313f1079A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000058313, ENSMUSP00000088071, ENSMUSP00000128870
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr3:27383251-27385891 
LOW PSI
HsaINT1042112
(SLC4A7)
Human
(hg19)
chr3:27424742-27427382 
HsaINT0153489
(SLC4A7)
Rat
(rn6)
chr15:11840618-11844167 
ALTERNATIVE
RnoINT0138556
(Slc4a7)
Cow
(bosTau6)
chr22:1758703-1762752 
LOW PSI
BtaINT0136154
(SLC4A7)
Chicken
(galGal4)
chr2:39025861-39026473 
ALTERNATIVE
GgaINT0101760
(SLC4A7)
Chicken
(galGal3)
chr2:38442425-38443037 
LOW PSI
GgaINT0101760
(SLC4A7)
Zebrafish
(danRer10)
chr16:42796759-42797715 
LOW PSI
DreINT0151598
(slc4a7)
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"