Special

MmuINT0151672 @ mm9

Intron Retention

Gene
ENSMUSG00000026532 | Spna1
Description
spectrin alpha 1 [Source:MGI Symbol;Acc:MGI:98385]
Coordinates
chr1:176149897-176152830:+
Coord C1 exon
chr1:176149897-176150105
Coord A exon
chr1:176150106-176152709
Coord C2 exon
chr1:176152710-176152830
Length
2604 bp
Sequences
Splice sites
5' ss Seq
AGAGTACGT
5' ss Score
6.58
3' ss Seq
ACTTTCTTCCTTGGTCCCAGGGA
3' ss Score
8.8
Exon sequences
Seq C1 exon
GACCCTCTCAAAGATCTGAATGACCTGGCTCAGGAGCTGATCTCCAGTGGGACTTTCAACATTGACCAGATAGAAGAGAAAATGAATGGTGTCAATGAGCGCTTTGAAAATGTCCAGAGCTTGGCAGCTGCACACCACGAGAAGCTGAAAGAGACGTATGCCTTGTTCCAGTTCTTCCAAGACCTGGATGATGAGGAAGCCTGGATAGA
Seq A exon
GTACGTATCACCAGCTCACTGGGTAATGCACCAAACAGATTCAGTGCATGCTGAAGTCAATTTGTAATTGATTTTTATGTTGATAATACTTTTAAACCACTGCCTCTGCTGAACATATACATTGATTTCACTTTTCACCTTAAATGGATACAGGCAGGAAACCAAGTGCAGCGGCAGATAGGAAGGAACAGTTTCAACCACATTCTGGGAATAAAATTGAAATACCATACATTTTTTTTTTAAAGAAAAGAACAGTTTGTTGAATTATATAGCACATGGAAAGCCAATTCTTTGCAACTAATGCAGAAGACCACAACATGGTCATTATTATTTTCTTTTTAATGATGTATTTTTTATTTATGTGCATATGAATATGTCAGTGTATATGTGTCCTTACATGTGAGTGCTTATGGAGGCCAGCAGAAAACATAGAGTCTCCAAGAGCTACAGTTGCAGGTTGCTATTGAGCCTCCTGATATGAGTGTTAGGAATCAAACTGCAATCTTCTGCAAGAGAAGCAAGCATTCGTAATAACAAATCCTCCTCTCCAGCCCCCAGTCATTACTCTTTCTATACTTGTTGCATAATATGTGACTGTAGGCAGTCCCACCATCTGTCATAGTTTCAGTGCTGACCCCATCCCTTTAAATATGGCTGGGAAATTCTTAGCAAAGCAGGAGTTTTTGCCTGTTTCATAGTTACTTTGTTCCTTTTGTTTCTCAAATGCCGGTCTTCAGATTCTTTTTTTTTCCCCCCCAGTGGATATTAGCCCAGAAATTTCTTTTTTTTTCTTTTTTTTTTCCTTTTTTTTTCCATTTTTTATTAGGTATTTAGCTCATTTACATTTCCAATGCTATACCAAAAGTCCCCCATACCCACCCACCCCCAATCCCCTACCCACCCACTCCCCCTTTTTGGCCCTGGTGTTCCCCTGTACTGGGGCATGTAAAGTTTGCAAGTCCAATGGGCCTCTCTTTCCAGTGATGGCCGACTAGGCCATCTTTTGATACATATGCAGCTAGAGTCAAGAGCTCCGGGGTACTGGTTAGTTCATAATGTTGTTCCACCTATAGGGTTGCAGATCCCTTTCGCTCCTTGGGTACTTTCTCTAGCTCCTCCATTGGGAGCCCTGTGATCCATCCATTAGCTGACTGTGAGCATCCACTTCTGTGTTTGCTAGGCCCCGGCATAGTCTCACAAGAGACAGCTACATCTGGGTCCTTTCGATAAAATCTTGCTAGTGTATGCATTGGTGTCAGCGTTTGGATCATAGCAGCCTTATTTATAATAGCCAGAAGCTGGAAAGAACCCAGATGCCCCTCAACAGAGGAATGGATGCAGAAAATGTGGTACATCTACACAATGGAGTACTACTCAGCTATTAAAAAGAATGAATTTATGAAATTCCTAGCCAAATGGATGGACCTGGAGGGCATCATCCTGAGTGAGGTAACACATTCACAAAGGAACTCACACAATATGTACTCACTGATAAGTGGATATTAGCCCAAAACCTAGGATACCCAAGATATAAGATACAATTTCCTAAACACATGAAACTCAAGAAAAATGAAGACTGAAGTGTGGACACTATGCCCCTCCTTAGAAGTGGGAACAAAACACCCTTGGAAGGAGTTACAGAGACAAAGTTTGGAGCTGAGATGAAAGGATGGTCCATGTAGAGACTTCCATATCCACGGTCTTCAGATTCTTACAGGTAGCACATAAGTTAGAAGGAAGCATGTTTTATAAGGTGTCAAATAGGACCTTTGAGTAGTCATAAAATACCATAACCTTTCGGTGTTCAAAAACTTCATGTAGTTTGTAATGCTAAAGATCAAGTGCAAGGCTTTGTATAAGCTAGAGCAGTTTTCTACCACGAGACTATATCCCCAGACATGATATTTATATTAATACACAAAATAATGAAACTCATATAATTTTCATAGTGTTCAAAAGAGAAAACACTAATACATATTCTAGAGTACTAATGGGAAGACTGTTACTGCTATATACATGCTGGACATTGGTATGTTATTTTCATTTTGGTGACATAAATCAAGTTTTCTAAAATTCTCTTCCACTACTTACCTTTTGGTTGTTGATTCCTGGATCAGTAAAGGGTTTGTTACTGTTATTAAAAAAAAAAAAAAAAACACCCTGACCTAAGCAACTTGAGAAGCAAAGGATTTCTTTCAGCATACAGTTCAACGGCCGTCTTTTACTGAGAGAAGACAGGGCAGGAAGTGAAACAGATCAGAAACCTGACTATAGGGGCTGATGGCATAGACCATGTATGAGTGCAGTTTACTGGCTTGTTCCTCATGGCCCATAGTGAACTCAGTTCTCCTACAACAATCAGCAATTAAGAAAATGCACCACAGTCTTGGCCACAGGCCATTATTCTGAAGACATTTTCTCAATTGAATTTCCCTCTTCCCAATAACTCTAGTTTGTATCAAGTTGACATAAAACCAGCCAGCACAGTCCCAGTGTTCATCAGAACTTCAGCTCTCACCATGCATTCACATAGACATCTATTGTTCTAGTTTCATCTCAGATATATCTAACCTCTGATTTTCCCACTTTCTTCCTTGGTCCCAG
Seq C2 exon
GGAGAAGTTGTTACGAGTGAGCTCCCAGGACTATGGGAGGGATCTTCAGAGTGTTCAGAACTTATTGAAAAAACACAAACGCCTAGAGGGGGAGCTAGTGGCACATGAACCTGCTGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026532-Spna1:NM_011465:36
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:
PF0043516=Spectrin=PD(47.6=71.4),PF0043516=Spectrin=PU(16.2=24.3)

							
A:
NA

							
C2:
PF0043516=Spectrin=FE(38.1=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000027817f1935A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000027817
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:158636762-158638032 
ALTERNATIVE
HsaINT0158337
(SPTA1)
Human
(hg19)
chr1:158606552-158607822 
ALTERNATIVE
HsaINT0158337
(SPTA1)
Rat
(rn6)
chr13:92304557-92306155 
LOW PSI
RnoINT0142966
(Spta1)
Cow
(bosTau6)
chr3:11182187-11186004 
BtaINT0140395
(SPTA1)
Chicken
(galGal4)
chr17:5174553-5175335 
LOW PSI
GgaINT0124383
(SPTAN1)
Chicken
(galGal3)
chr17:5801365-5802147 
LOW PSI
GgaINT0124383
(SPTAN1)
Zebrafish
(danRer10)
chr21:13098896-13099798 
LOW PSI
DreINT0155193
(spna2)
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"