Special

MmuINT0139961 @ mm9

Intron Retention

Gene
ENSMUSG00000019124 | Scrn1
Description
secernin 1 [Source:MGI Symbol;Acc:MGI:1917188]
Coordinates
chr6:54472754-54475705:-
Coord C1 exon
chr6:54475503-54475705
Coord A exon
chr6:54472949-54475502
Coord C2 exon
chr6:54472754-54472948
Length
2554 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
ACACATCGAACTCTTTGCAGAGG
3' ss Score
6.06
Exon sequences
Seq C1 exon
GCTTGGCTTAGAACGAGGGACAACAGCTAAAGAAGCCCTAGACATCATTGTTTCTTTATTGGATGAGCACGGACAAGGTGGAAATTATTATGAAGATGCCCACTCCTGCCATAGCTTCCAAAGTGCATATCTGCTGGTGGACCGAGATGAAGCCTGGGTGCTGGAGACTGTAGGGAAGTATTGGGCTGCTGAGAGAATCACAG
Seq A exon
GTAAGGGGGTACAGGATAAAGACTTTTGATGATAGGACACCCTGAAGTTATGCTGGTCAGACATGCTGGGCTGGCCCAGAAGAGCTGTGGTGCTGTGGTCCATCCTCTATGCATCCCGCTTCAGGCTTAAGCATGCCTTTCACTTCCAAGTACCTGCTTGCAGAGGTGTATCCGGAGTCTCCTGAAGGGATATCAAGCCTCAGAAAGTGCCCATCTAATTCTTTACATTTCCTGTTTGCTTTTTTGACATATCTAGTTTCGACTATAAACCATGACTATGGGTTAGGCAAGGGAATGAGGAGTCTTGGATCATAATAACCAATCCCTTGTCACTCCTGGCTCCACAGCTGTTTAAGCTTAGACTCATCCTCTAAAGTAGAAACTTGGGTCTGTGAACACTACCGAGTGCTACTGGGTGCCAACCAGGTCACACATCTGAGACTCCATCCCTAGGAGGGCATCATAGACTTGGCCATCTACATGAGAAGTGCCCCTCTGGTTCATGCTGCTTCTTGTTTCTGGTTCAGTGCTGAGACAGTGTACCACCACTGCAGGGCTCTCCCTCAGATTCCCAATCGGATAGAGTACTAGAATTGGCTAACGGGCTCCTGAACGTCCTACATACCTCCAAAGAAAACTGGTCATTGGTGGTCCCTTTGCACTCCTTGCGACAAGATGATAAATACACACTGTGTGCATCAACATTCTCCCTTCCCAAATTCGAGGTATCTCCGGCTAGTAGGGCAACTCTTGTCCTTTTCTTGAGCCTCTACACCACTGCATACTTTTGTTCAGCTGAGTTTATTATGAAGTCTTTACCAGTTAATTATGGAAGATATTAGGTATGCAATCTGTTTGCTACTCCAGTTTTTAGATAATCAGAACGAAATCAGACCTTAGCCAGATCTTGGCAGTCACTGGGAGTCAAACCTGGTTTTGTGCACGGGTTCCAGTGACGGAGGCTCCCCCACAATTAGCAAATGTTCTGTGCACAAAGTTATCCTGCTGAGAACAAGAGGGTAGACCAGTTCTCTGTGTGCGTGGAGACTGTGTCTTCTCATTCTCACAGGATGTGGAACAGGCTAGCAAAGCCATCAGCGAGTTTTCCTACCTCCATGGCGTGCCCAGCATATTTCTCAGGACCTGTGCACGATTCCTGGGGTCTTAGAGCGTTTGCAGAACAAAAGGTTTCCCCTCCCACCCCCAGACCTCCAGCTCCCCTTCCCCTATAGGAACTTAAAACTCCTTTACACAAACCTCCCTGAGATAAAGCAATGCTATCAAATGGCTCTCCCGGGAAAGCGGATGGGCTGTGCTTCAAAGCCATCCAGTTGCTTTTAAGTAGAATCTAAGACTTTTTGATCTGTAGCTACATTCAGAAGCACGGCTTTCTTCAAAGCCTCGCTTATAAAGGTCCATCTCTACAAAATGAGTGTTGTTTTTCACTAAACATTTTTTTTTTTCGAACAGCCATTTTTTTCCCTCTCATCAGTTTCATGTTCTCTGACTCCAGCAGCAATAGACTGATGGCGGTAGGAGTTATTGAACTCTGTCCTCTCGGTTCTGATTCTTTAAAAAACAAACAAACAAACAAACAAACAAACAACAACAACAAACCAAAACCCCCAAACAAGTGTGTACTATAAACTAGCCTCTAGGAAAATAACCTCAGTGGAGTTCTCAAGACCCTTTCTTTCTTTGAATCGCTCAGCATGAATGGTCTCAATATCACTGTTTTTTGTTTGTTTGTTTGTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTGGATCATAACTGTTTTCTGTTGCTTAATTAGAATTTTACACTAGTGATACCCTTTAGGAAAAAAGGAGCCTGTCAGTCAAGAGTGAATAGTTTGGAGGTATAAATCATCAAAACAAGGAATCCTGGGAAAAGGGTCCAGCTGACTTGACTTCAAGGCACCCGGATTCAGGCTGTAAGGGTTCTACTGTGGTGGGATTCAGGCAGAGAGAGCTCTAAGGTAGCCTTTTCTTTCTCACTTCATTCTCCGGGAATTTGGAAGCTCGGCACACTCTCTGGGAGCAGCCTCTGTGATTTAGCAATGGTGACCCAGCCTCCGCAGTCTAGACAGCACCTTGAAGCTTAGCGACCAAGTCGCCCTTCACCTGTCTGAGGGTATGGGGGTGGGGGTGGCAGAAGTGTTCTTCCGGTAGGAGCGTGTTCCTGGGGAGAAGGAGCCTGTGAAGGTTGTGGCGTAGCCCCGTAGAGGAGCCAGACATATATCCCGAGTTTCCTGAGAAGTCCTTCCAAAGACCTGTTCAGTTTCCCTGTCGCCATGTATGCTTGAGGCTTATTCAGTCACAACGAAAGGCCTTGAGTGTTTGTGAACTTAAGATCAGTGAACGTGACGTCCATCTAAGCTGTAACAATGTCCGATGGAGACAAACTGAACCTTTTGGGATGTCTCCTGGAGGGAGGATCAAGGATTTTGTGCTTCTCTCTTCAGAAATGGCACTGATTCCTTCCTGGAGTCTCGGCTCCCTTTCACTAACCACACATCGAACTCTTTGCAG
Seq C2 exon
AGGGAGTGAGGTGCATTTGCAACCATCTTTCCCTCGCGACTAAGCTGGATGAAGAGCACCCAGAACTCAGGACTTATGCTCAGAGTCAAGGCTGGTGGACGGGAGACGACGAATTCAACTTTGCCCAGGTTTTTTCTCCAGCCGATGACCGTTTGGACTGCTGTGCAGGCCAAGACAGCTTAGAAAAGCAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000019124-Scrn1:NM_027268:4
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=0.030
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0357710=Peptidase_C69=FE(35.1=100)

							
A:
NA

							
C2:
PF0357710=Peptidase_C69=PD(27.8=81.8)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000019268





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:29940877-29943976 
LOW PSI
HsaINT0146134
(SCRN1)
Human
(hg19)
chr7:29980493-29983592 
LOW PSI
HsaINT0146134
(SCRN1)
Rat
(rn6)
chr4:84695886-84698306 
LOW PSI
RnoINT0131855
(Scrn1)
Cow
(bosTau6)
chr4:66833087-66834056 
LOW PSI
BtaINT0129697
(SCRN1)
Chicken
(galGal4)
chr2:34387942-34391508 
ALTERNATIVE
GgaINT0096079
(SCRN1)
Chicken
(galGal3)
chr2:33827944-33831510 
ALTERNATIVE
GgaINT0096079
(SCRN1)
Zebrafish
(danRer10)
chr9:2517228-2518462 
LOW PSI
DreINT0131726
(scrn3)
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"