Special

MmuINT0039325 @ mm9

Intron Retention

Gene
ENSMUSG00000026141 | Col19a1
Description
collagen, type XIX, alpha 1 [Source:MGI Symbol;Acc:MGI:1095415]
Coordinates
chr1:24310295-24313152:-
Coord C1 exon
chr1:24313099-24313152
Coord A exon
chr1:24310340-24313098
Coord C2 exon
chr1:24310295-24310339
Length
2759 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAA
5' ss Score
6.82
3' ss Seq
AGCCTGTGTCTCTCTTGCAGGGT
3' ss Score
11.29
Exon sequences
Seq C1 exon
GGCTTAACAGGAAGAACTGGACATCCTGGTCCCACTGGAGCAAAAGGTGACAAG
Seq A exon
GTACAAAGGAAAATGGGGCTTGGGTTAGGGGTAAGGTGGGACCATTGACTGTGAGCTCCATTCAATCAAGGGCAGCCTACAAGAGCAAATGACGTATGCTGGGCAGAGGCTACTCGTGGAGTGGACTTGCAAAGATGTTGGTCTAAAAGTGGGTCCAAACACAGGTGTTCATAGATGAGAACTCTGGGTTTGGAGATAGAAAATCCAAACGGTTTAGAAGCTGAGACATCCGTTTGTGAGGAAGGGTGACTGGTTCAAGCCTCCTAAAGAGGTAAAGGTAAGCTGGATTGTAATGTATTAGAGACTTCCAGCTATGGCTGTCTTGTTCTCTTTGGACTTTTGTTATATATATATATAAAGCTAGAAAATCCCCCACCAAAGCACTGGTGGTTTTGGTAGCTGGCGGGCCCATTTTCTTATTCACAGAGGGCATGTTCTAAAGGAGTCTTTGTGTGGTTCAACAGTAACGAAGCTCTTTCAGGCTTCTTTATAAGGGCACTGATCCCATTCATGAAAGTTCCACCCCATGACCTATCTCCTAAAGGGCCCATCTACTTCGTCGTCCTATGAGTAGGATTCATGCTGTAAGTTTAGAAGAGGAAAGCCCAAACATTCCAAGCAAGCTCCCTGGCTCCAGATGATGTCTTGCTGGCTATCAAGACAACGATCAGTAACCAAGGACTTGTGAGACAGTCTGGTAATGCTGTCCCTAAAAGACCTTGGCAGGAAATGACTAAAGCCATGTTCCCTTGGAAGAAGAATGTATTAGTTACTATAGTTGCTATGTCAAAATATCTGAGAAAACCGACAAAGGTGGGGAGGGTTTATTTGCACTTACAGTTCAAGACCTCAGTTCATCGTGGTGGGGAGGTCATGGTAGAAGAAAGATCTTGAGGTCTTCAGTTCACGTCTACCGCATCAGAAGGCAGGAAGCAGAGATAACTAGTTGAATACAACTGTTCTACTCCCTTATTCAGTTGGGCCTCCAGCCTGTGTGCTAATGATGCCCCTATTCAGGGTGGGTCCTCCTACTAAACTTTTCTGGAAACACCCACCCAGAGGTGTGTTGCCATGGTGATTCTAAATCTCATCCAACCGACAGTGAGGACCAACCATCACAGCTCACAGCTGGGTGTGTGTGCTGTGGCTGGGAGAGAAAACCAACAGCATGGGAGCATCAAGCTGTCATGGTGTAAGATCTCACTTCCAGGCATTACAGTGACCGTCCAGGCATAGCCACCGAATGGATGAAGTAGCTACAGCTATTCAGATTAAGGAAATAAGTGCAAAGAACTACAGAAGCTGCTTAAGTGTCTCCTGCACGCACGCTTGCCAGGATGCCACATCCTGAGCAGAGGGAAGCGTGATGGAATCAAGATCCCCGAGGCACTGAGAGGAAGCAGTGTGCTAGAGAGCCTCAGCACATTTTTATCCTGTTAAGATCTTAAGGATCTCTCTGTCCCAGCCCCTTTCCTCTATTTTCTATGAAAATTATTCAGCCCTTGATTTGCCTTTGAAGCTAATGGGAATTCCACACTGAAATGAGCATGAGGGCACAAATGAGAATATTCCTTCTGATGGTGCCAGGGGGTGGGGAGGAGTGTTCTCGACAGGCACATATTGTTTGTTGACTCATGAGAAGTGTGATGTAATGCTCTGAAGGGCATTGGCAGAGGTCAACAGAACAGGGGGAGTCTTAGGGGGACGGCAACCATCAAAGCTGTGTGGGAAAGATACAGCACACTTCCTCAGCGTGCGTGCACGTGCTCGGGCAGTGCATCGCGTGAGAAACTTTACTGTTTATGTACAATGATAAATATATGGTTTGTGATGTGTTCCTTTGTTGGTAGGAAACAGATGAGTATTGAAATAAGATCTTCAGTCCAGTTCTGAAAGAGGACTGACATCCCTCAAAATTCCTGGGCATCATATGCTCTGTGTTGTCACCATCCCTGATAGATGTGACTTAGAACAGTTTTATAATGATACCATTCTAAAAGCAGTGCGCAGTTATAGGAACGACTCTTAAAAAGCCAAAAGAGCTGCAGCAACTGCTTCCCATGAATGGACTGGTCAGTATTTCTGTGCTTTGTAAAAGTCACTTACCAGGTTTCAGTTCAAAAAAACTCACAGAATAGTTATTGGCCCAGTAAACAATTATTGGAGTCCCACTTGCCTTTAGATTTATGTCTCCTACAAGCTATTTACACTGTACAAACCATTTCCCTTAAATAGTGTCATAGCAAAATCATCACTTCCACTCAGTCAAACACACCTCACCTGGTTCGATATGACACTGGTTGGGACTTCATACTTCAGTTGCATATTCCATTATGAACTTGAGGGAGTGAAGATGAAGCCAAAAGTAAAGATTAATCCAGAGAGCCACAGTCTCCAAGTCCACAATTTATTCACATGAACTCTACCCTATCCCCCACGCTCACATAGGAGGAAAAATCCCCCACCTGTACTCAAAGCCCAGGGCAGGTCACCTAACTGGTCTACCCCCAGTGAAACTGTCACTCCTAGAGTTCGCACAGCGAGAATCCAGGTGGACTTGAAAGGGGTTATTCACTTTCCTGGAGTGGGGAAATGTATTTTACTGGGTTAAGAAGCAAGCTAAGCAGAATAGGATCGCAAGGCTGAAGCCAAATGACAAGCCATGATGATTTCGGAAGATTGCTTTCTGAACAACCTGGTTCACAGACTTGGAGTAGAAATGGCCAAACCATTAATTCAAGCCTGTGTCTCTCTTGCAG
Seq C2 exon
GGTAGTGAGGGACCCCCTGGGAAACCTGGACCTCCTGGACCCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026141-Col19a1:NM_007733:36
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(25.4=100)

							
A:
NA

							
C2:
PF0139113=Collagen=FE(20.9=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000110899





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000052606
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:70163397-70165940 
ALTERNATIVE
HsaINT0038346
(COL19A1)
Human
(hg19)
chr6:70873289-70875832 
HsaINT0038346
(COL19A1)
Rat
(rn6)
chr9:30553944-30556718 
LOW PSI
RnoINT0039236
(Col19a1)
Cow
(bosTau6)
chr9:9454229-9456365 
BtaINT0041182
(COL19A1)
Chicken
(galGal4)
chr3:82326614-82328834 
LOW PSI
GgaINT1009984
(COL19A1)
Chicken
(galGal3)
chr3:85683436-85685656 
GgaINT0087779
(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"