Special

MmuINT0140492 @ mm9

Intron Retention

Gene
ENSMUSG00000026924 | Sec16a
Description
SEC16 homolog A (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:2139207]
Coordinates
chr2:26264951-26268433:-
Coord C1 exon
chr2:26268356-26268433
Coord A exon
chr2:26266474-26268355
Coord C2 exon
chr2:26264951-26266473
Length
1882 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TGCTGTTCCTTTTGTTCTAGGCT
3' ss Score
10.29
Exon sequences
Seq C1 exon
GCTCCTGGAGACCATTGTCCTACAGGGGCCCCTCATGGTGGGTCTGTGCCCTTTTACAACCCTGCTCAGTTGGTGCAG
Seq A exon
GTGAGTGACCCTTGCCTTTGTTCCCCACAGCCCCAACTTTTCTGCTCAGTGAGTCTCCTTTGTTCCCTGGCTGGCTGTACTTTTGGGGGGGTTTGTTTTGTTACTTGTTTTTTTTAAAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTAGAACTCACTCTGTAGGTCTCTTACTTGACTTAGTCTGCATCCTATGCTTGCCTGCTGCTCCTCTCACTACTCTGGGCTCTTCAGGGTCAGGGATTGTTCTTTTTGTTACTTGCCATGGCTGAGGGTTGGCTCTCACTATTGCCAACCTCCCATTCCTGCACAGGATGCATGGTTTTCCCAGGTTAGCCATAGATCACAGGCTCTAAGCCCAGTCCTCTCCCTCCTGCCTCCCCCTCTTCTCCTTAAGAGCAGCTCTTCCAAGGAGACCCCTGGTTTGGGATTTTTCATTGCTTCAATTCCTCTGTCTGAGTGACACATTGTTTAATTGCTTGACTCTTGAAGATCCTTTGGGTCTGCCCTAGGTGCTGGGTTGAGAGTTTGCTGGGTGCAGTTTTTAGATCAAAAATGGTAGTACCATTTTCTGGTGCTCACTGTAAGAGAGTCCGGGTCTTCATTCTCTGTCTCTGAAGGCTGGAATAGCATCTTCCTTGAGGATCTGTACACCCCTTCCCTCAGTCATGGCTCTTGTGTTCTTCGCCTAGGAGAGTCTGGAATGTGCTATATAGTTTCTCTCCTCCACCATCTTTTGAAGAAGTATAGTCTGGCTTCTGTGGAGGGGACGAGCTCTAGGCAAGCATCTTTATTTTGGGGGACAAGGGACTTAAACCAGGTACTTAAACATGCTGCACAAGTACTCTAAAAAATGAGATGCAGTCCTGGGGAAAGCAGCATGTGTGGGGTTTTTGTTGTTGTGTTTGGTTTTGTTTTTAATCAAAGGGCAAGCAAGCAAAGTTTATTTAAATTTTTATTTTATGTGTATGGGTATTTTGCTGCATATATGGCTGTCTACTATTTGCATACCTAGTGTCTACAGAGACCAGAAGAAGACATCAAGTCCCCTGAAACTGGAGTTACAGATGGTTATGAGTCATTATGTGGGTGCTGGGAATTGAACCCAGGTGATCTGGAGGAGGAGTCATTTTTTTTGTTTTGTTTTTCATATATGTCATACAAAGTCTATTGAGAAGTAAATAAATCTTTGCAACCAGGAAGAGCTCAAAATGAGTTACCTGGGCAGGTATCTTGACATTCTGAATGTGATGTTCTCAGCCCACTCTAACAGGGACCCTGCCCGCAGCTGTGCTAGACCCAGCCTTGGCCACTCTCTGTTTAGTCCTCTTGAGGGGCCTGGGCCCTGTGCTAAGCCCTGTGCAGATGAGGCTGCTGATATCAACATTTTTGTCCATATTTTCAACTCCAAGATCTCATTTTTCTTTTGAGCTTGTGGTTGAATAGTTCTGACAGATTTCTTGGATTAGATCCCAGTAAGGTCTAGTGAGGGAGGAAGAATATATGCAGTGTTCTCTCGTGGCATGCAGCGTCCTTGTGCTTTCAGGAGTAGAAAATTATAGGCCACTGGCCACCCTTGCACTCAGTGAACCCTTAGCTGCCCCCCCCTCCCCCCCCCCCCCCCCCGCTCTGTAGTGCTAACTCAGCTCTTTTGACCTTGACAGAATTGGCAGAACAAAAACAAATCATGTCTGCAGTGCTGTGGGCTAGGAAATGCTGAGCAGCAGGAACTTGGCACATACAGAAGGTCTTGCTTACACTTGAAGCTAACACAGAGTCTGCCCATTTGTTATTGATCTGTGGGGTTATCCTGTAGCTCCATCGCTGGACAGCCTCTGGGCATGGACACATGTAGGTCATTGCTGTTCCTTTTGTTCTAG
Seq C2 exon
GCTTCTGTCACCTCGGGAAATTCAAGGCCAGGGAGGATTGGCCAAAGAAAATATGCGGCATTGAACTAGGATTGCTGCTGGATTCTTATTTGGAACCCTGAGATGATTAGATAACTGTTCTTCACCAAGAACCAACTAGCTGCCTCAGGTCTCGTGGATCCCAGATGGACATGGCAGTAACTCAGAGCCGGTCATACTGTGTGTCTCCTTCCTTGCAGCCTATGTATATGAATGATTGAAAAATTGATTTCAAGGTTCCTTTCAAATGCTGGATAGAATGAATCTAATTCAAAGTCTTTTATGTAAAAGAACAATGTTTCTTTTTTAGTCACTTTAGACAAATTAAGGTTTGAGCCACTTGAGAATATCCCCGCAGAGAGGCTAGGCAGGGATTCACTACAGGAGAGCACAGTTACTTGGACACCAAGGCCTTTCTCACCTGAGAAATGGTGCAAACCAACCAGGGATCCTTAGGCTACTGAGAAGGCTGTCTGCTTACCTGGAGAGGACTGACTGCTGGGATGTCTGGCCTAAGAGGAGCCTCAAACTGCACTGGGCAACTGTGCCTTGTCCTGTGAACTGGGGAGTACATGCCAGCTCCTCAAAGGGTCACCAGATGGCAGCGGCTCCCAGGCTGGGGAGGAAGTGGTTACAAGGGCATGTCTCTCCAACATTTCCAGCCTCACTCCATTTTCTGTGGCCTCATTAGTGCTGGGTGCGTTTTTTTTTTGCTCCGAGCTTTCCGTCATGGCTCAGTCACTGGGGAGAGCCCCAGGGAGCTGATATTCTGAAGCTGCTGATCTGATTAACCAGGTCAAAAACTGGCTGTGTGCTGCAACGTACTGCCCTCCTAGCCAGGAGTCTGTATGGAGCCCTCTAGCTGACTCAATGTCACCTGCAGACAGCACTTAAAGCCTTGGTGGTATCTTGGAGTGGCTTACGGTGTCCTAGCGCACACTCTGGAACCTTGCATCTCTACCCCAAAGCCCACCAGGGACCTTCAGCAGCGACTCACTGGCTCACCCATATCACTTCAAGGAGCTGCCACCACATAAGAGTCAAAGCTTTAAGGCTTCACTGACTGTTCCTAAAACTATCCTTACACTCTAAAGAGGAAGGGAAAGAGAGTTAAATATTTAAAAATCAGCAGGTAGAAAACATAAATGGTTTGTTTGGTATTAAATTTAGAAATTGTAGAACATGGAATTAGTACAGCCCTTCCCGGTTTTCTGGTTCCTTGCATCATCTAGGAAAGACTCACAGAATGGCTTCCAGGACGTTCCATAGATGAGTGTACTTGGACCCTCCTGTTCCTGTCATTAAGAAAGGCCTGTCCCTGTGGGTCAGTAGCAACTTGTGTCCTTGCTGGGACCAGGCAGGACCCTTGCCTCTGGTTCAACCCTGCCCAGGCTCTGTGTTGACTGCCAACCACTTTGGATTCAAGAAGCTTCCTCCCTGGGAGCTGCTATTTTTCCAAAATTCACATTGTTAAATAAAATATTTTGGGCTCTCAAGTAACTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026924-Sec16a:NM_153125:29
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.985 A=NA C2=0.988
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000109716





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000109716f2028A
          









    
Other Skipping Isoforms:
ENSMUSP00000028290, ENSMUSP00000088796, ENSMUSP00000122255
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr9:136441824-136443822 
ALTERNATIVE
HsaINT0146705
(SEC16A)
Human
(hg19)
chr9:139336276-139338274 
ALTERNATIVE
HsaINT0146705
(SEC16A)
Rat
(rn6)
chr3:3857744-3859884 
LOW PSI
RnoINT0132300
(Sec16a)
Cow
(bosTau6)
chr11:103939328-103940111 
LOW PSI
BtaINT0130201
(SEC16A)
Chicken
(galGal4)
chr17:7872143-7872520 
ALTERNATIVE
GgaINT0126254
(SEC16A)
Chicken
(galGal3)
chr17:8561239-8561616 
LOW PSI
GgaINT0126254
(SEC16A)
Zebrafish
(danRer10)
chr16:52040413-52044858 
LOW PSI
DreINT0135078
(si:ch1073-385i9.2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCTCCTGGAGACCATTGTCCT

				
R: 
TCCAGCATTTGAAAGGAACCTTGA

				
Band lengths: 
351-2233

			

		

	





	
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"