Special

MmuINT0039409 @ mm9

Intron Retention

Gene
ENSMUSG00000029661 | Col1a2
Description
collagen, type I, alpha 2 [Source:MGI Symbol;Acc:MGI:88468]
Coordinates
chr6:4470772-4471284:+
Coord C1 exon
chr6:4470772-4470879
Coord A exon
chr6:4470880-4471230
Coord C2 exon
chr6:4471231-4471284
Length
351 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
TCTCATGCCCTTTCCTGCAGGGC
3' ss Score
11.04
Exon sequences
Seq C1 exon
GGCTCTGTTGGAGCCCAAGGTCCTCCTGGTCCCAGCGGTGAAGAAGGAAAGAGAGGGTCTCCCGGAGAAGCTGGATCTGCTGGCCCTGCAGGGCCTCCAGGGCTTAGA
Seq A exon
GTAAGTTCTGAATCCTCCAGACACAGCAGACCCTGATGCCACCCCTTGGCTGGGAATTGGTCAGCATTTCTGCATGTGTTTCCTAGATGAAAGAGCATCTGTCTTCCATCTGTTTTATTACATTAGCAACTCTCAATTTAGTATGTTATTAAATTGGTCTGGAAACAGTGTTGACCTATTTTTGCAGGATGCTCATCTGTGCATTCCCTTGGCATTTGGGTAAAATGTTTTGGCTTGGTGTGCACCCATATCTTTCCTCTTAGGAGAAATGGTGCCCTGTCTTAGGAAACTCTATCTGATGAGATCTAAAGATTTCTCTAATCTCCTGCCATCTCATGCCCTTTCCTGCAG
Seq C2 exon
GGCAGCCCTGGTTCTCGAGGTCTTCCTGGAGCTGATGGCAGAGCTGGTGTAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029661-Col1a2:NM_007743:21
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(29.3=80.6),PF0139113=Collagen=FE(48.6=100),PF0139113=Collagen=PU(8.3=19.4)

							
A:
NA

							
C2:
PF0139113=Collagen=FE(23.6=100),PF0139113=Collagen=FE(20.2=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000031668





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000130377
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:94410528-94410888 
LOW PSI
HsaINT0038430
(COL1A2)
Human
(hg19)
chr7:94039840-94040200 
LOW PSI
HsaINT0038430
(COL1A2)
Rat
(rn6)
chr4:29544108-29544461 
Cow
(bosTau6)
chr4:11640204-11640574 
LOW PSI
BtaINT0041266
(COL1A2)
Chicken
(galGal4)
chr2:23719639-23720518 
LOW PSI
GgaINT0097669
(COL1A2)
Chicken
(galGal3)
chr2:23548561-23549440 
LOW PSI
GgaINT0097669
(COL1A2)
Zebrafish
(danRer10)
chr19:41404928-41405561 
LOW PSI
DreINT0049441
(col1a2)
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"