Special

MmuINT0039343 @ mm9

Intron Retention

Gene
ENSMUSG00000026141 | Col19a1
Description
collagen, type XIX, alpha 1 [Source:MGI Symbol;Acc:MGI:1095415]
Coordinates
chr1:24533224-24536847:-
Coord C1 exon
chr1:24536767-24536847
Coord A exon
chr1:24533350-24536766
Coord C2 exon
chr1:24533224-24533349
Length
3417 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
ATTCTCTTTGGGGATTTTAGTGT
3' ss Score
4.16
Exon sequences
Seq C1 exon
ATCGAACTTCACCAACTTAGAATCTACTGCAATGCAAACTTCCTAGCTGAAGAATCATGTTGCAACTTATCACCTACTAAG
Seq A exon
GTAGGTTAATTTCCTTGCCATGTGAAACACAAGCAGTGAGATATATTTCAATTGGCATTCGTCATCTGTAGGTTCTATGTGTAGGACTTTGTGAAGCATCTCAGTTGAAACTGGGTGAGTAATTTATTCTCCGTATGGAGCCATTCTTAGAACCAGCTCAACACTTCAACCACAGGGTTGCACACTGAAATTTGATGGTGATTTGTGCTCAGGTTGGTCTCAGTGTAAGAAGAACCAGTCTTTTTGTTTGTTTTTTTCTGAGACAGGGTTTCTCTGTATAGCTCTGGCTGTCCTGGAACTCTCTCTGTAGACCAGGCTGCCCTTGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGCACCACCACTGCCCGGCGAGAACCAGTCTTAATGTACACCTTCCTGCCACCCACTGTACCTGTTGCCTTGTCTCATCTGAGGCCCCAGCTGATTGGAGGTGCTGTCCTGGGCATCTTTTCTCCTTCAAACCACTGCACAGGAGGAGTGTTCCATTTCTTGATTTGTCAGCTACAAAATGAAAGGCTTTCAATAGGGAAAAATTATTTTTTAAAAACCCTCCTCAAAATAACATATGAAAACCAAAAGTCCAATATTCAATGAATTGTTTCTTTGGATCTTAATTTCTCCAAATTTTTACACTTCCTAAGAAATCTATATGAAATTTTTAATCAGTGATTTTTTTTTCAATTTAAAAACCCTTGTAACTTCTTTCGTGTGGTGTGTGTACTAGAGTGAAATCTAGCCAAATAACTCAGAGTCTTTCAAATATTATGCCTTGCTTATATAACTTGGCTATATAAAGCATATCTCAAACCCAATTTACGGATCTCATTCCAAGTAAAGTGAAAGTCTGCCAAATATCTTTCTTTAAATACCTAAAAAGATAGCTCAAATGCCAGTCTACAGACCTGAAATACTGAGGTTTCCTGAACCTATACCTTTAATCATTTTTCTTATTTCAAAAGTGTATTGTAAATCATTATGAATGTGTTATATTGGAGTTCTTAAAATAACTATTTTCTTTCACTTAAAAGTAATGTAATGATGTTTTTATACTTATAAGTTTTATATTCTTCTTCATTATTCATTGCCTTATGTTAATAGATTACTATGAAAACAGGTTAGAATAGAAATGGATGAAGAATTGGATGAAGTAACAAGTCTGACATGACTTCACACAATAGTTTAGTTCACAGTGCTAACCTTAAATTTTAATAAAAAGATAAATAACAATCTTTACAAGTATTATTTGAAAATCAGGTTTACAGTTGAAAATAAGTTAAGAATTTAGTCCAAGTATGTAAAAATAACCAAACGATATTTTTTATGTTGATGATCATTTGTGATGATCACATCACCATCCATTCTGAAATTAAAAGTAACTAGAACTCTGATACATTTTTACAAGCAGGAATACATAAATAAGATAATCCTAAAAGCCATTAAATACAGTGGATGAAGATTTGAAACCAACTGTCTTGTATGCTTTTTAGTTTTGAAAACTGTCTTAAAGGGGGCTAGAGAGATGTCTCAGTGTTTAAGAGTGCTTGTTGTATAGCCATGGTGAGCTGAGTTCTTGCTCATCTCTTAGCCCTGATACTATAGTGGGTGGGCAAAGACAAAACACCCCTGAGGCTTGCAGGCTGCTACCCTCTTCTAAGACTACAAGTGTGTGTTTCAGGGAGAGACCCTACTGCAAAGAATAAGGTAGAATATGATAAAGGAGGACAACTAACCCCCCATTGACTTCTGTGGGAGCACACAGGTACACATACCTACACACATATATGCACACCACATACACATAAACTATACACATATTGACACCCACAATAAGTATATTCATAAACATATAAATGTCTAAATCCAAAAATGGCATTATATCTGTGCATTTATAGCTACATATTAATATTAAACCGCACATGCTATTTTCATGTTAATATTTTATGGAGTACTTCAAAGCTGAAATTTATTCCAGACTATCTATAGACATGTTCCACTTCTAATAAAGTCAGATTTTCAGTCTCTGAAACAATCAAATGTCACATGACTGAGGGTATAAAGTAAAAAGTGCATAGGAAATAATAAATCATTCAGGAGAAATGAACTGTGTAGCAATCTTGTTTCATTTGAATATAATTCTAGGTTATTAAATTGAAATTTTATTAAGATACCAAATGATTATTAAATATAGAGGCGATTAACATGGAATCTCTCGTTTCAAATATGAGAATATGGTCACAGTGTGTCTGGGTGTGAAGTTTATTGTGGGTCTTATTGTTACTACAAATATTAGAGTGATACCTATTATTCAAGAGTCATTTATGAATTCTATTTGAGAAAATGCAGGAAGGGAATAAACATCAGATATGAAGATGAAAATAATACCTACCGTGGGCTCACACCACAGTAGCAAGCCATTGACTTTTTATTTGCATAACTTGAATGCAGTTTTCCACTCATGTATAATTTGCATCCAGTGAGTTTTTCCATCTGTTGCTTCATCTTCACTGAAGCTTCAAATAAAGAGTTAGCCATGGGGAACAGCGTGGTATGAGTTGTCAGAACAAGAAGATAAATTGGAATTCCCTTTAGAATCAACATGTGATACTTCCTCTATATTTAAAAATATTTATTATATCTCTGTGTGTTGATATGCTTGTATGAGTGCAGGTATAGAAGAGATCATCAGAGGTTAGAGTAACAGCTGGAGGAGGTCTCCAGATGTAGGGCCTGAGAACAGGACTTGTGTTCTCCACAAATTAGCCCTGGCTTTTAACTGCTGTCTCTCCAGTCTCCTGCATGAAATTAGAGGGGGAAGATTCTGCCTATTTATAGCCGTGTTCAGCATGTTCTAAACTCACCAGGTTCAGAATCCTCCACTTTTACGTCTTTAAAGAACACTGGACTAGAATAGACTATATTGTAATTAGCCGTCTTAGAGTATAAAATAAATTCATTTCCAGCTTGACTTACACTTACCACCAGCTTGCTGCAGTGCCTATATTTTACCAACCAAATTTATATGCTTTTAAACTTTTGTTTGCCATATACTATTCACATTTTGCTTGTGTGAAGTATTTTATTGGAAGAATGTACTATTATTGATATATAATATCACTATACTTATCATAAGGCCACCTAATGTGGCTTTAAAATTTCTCAATAATCACTTTTCATATGCTCTTTGTGTGTAGTCAACATGGTTAAGTACACTGCAGGCTTAGTGATAGAGTAAAAAATGTAATAAACTTTTATAAATGGTTGGCAATCTTGGTTACTAAGAAGGAAGGATGGCAGGCATCCAGACATCTCAGCTTGATGGGAGCTAACTGCAAGAACTGACGTCATTCTCTAAATTCTCTTTGGGGATTTTAG
Seq C2 exon
TGTCCAGAGCAAGACGACTTTGGAAGTACTACTTCATCCTGGGGGACCTCTAACACTGGTAAAATGTCTTCATATCTGCCAGGAAAGCAGGAACTTAAAGACACATGCCAGTGTATTCCAAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026141-Col19a1:NM_007733:7
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=0.667
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF133851=Laminin_G_3=PD(7.1=40.7)

							
A:
NA

							
C2:
PF0139113=Collagen=PU(0.1=0.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000110899





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000052606
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:69932864-69936784 
ALTERNATIVE
HsaINT0038364
(COL19A1)
Human
(hg19)
chr6:70642756-70646676 
ALTERNATIVE
HsaINT0038364
(COL19A1)
Rat
(rn6)
chr9:30786284-30790559 
LOW PSI
RnoINT0039253
(Col19a1)
Cow
(bosTau6)
chr9:9152645-9158654 
Chicken
(galGal4)
chr3:82449366-82451023 
LOW PSI
GgaINT0087749
(COL19A1)
Chicken
(galGal3)
chr3:85806304-85807961 
LOW PSI
GgaINT0087749
(COL19A1)
Zebrafish
(danRer10)
No conservation detected
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"