Special

MmuINT1007510 @ mm10

Intron Retention

Gene
ENSMUSG00000048126 | Col6a3
Description
collagen, type VI, alpha 3 [Source:MGI Symbol;Acc:MGI:88461]
Coordinates
chr1:90807471-90810728:-
Coord C1 exon
chr1:90810126-90810728
Coord A exon
chr1:90808077-90810125
Coord C2 exon
chr1:90807471-90808076
Length
2049 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TGGTCATGTCTGCTTTTCAGGTG
3' ss Score
9.68
Exon sequences
Seq C1 exon
GTGAAAAGGATGTGGTGTTTCTCATTGATGGCTCTGAGGGTGTCCGCAGTGGCTTCCCCCTGCTAAAGGACTTTGTGCAGAGGGTTGTGGAGAGCTTGGATGTGGGTCCCGACCGTGTGCGTGTGGCACTGGTGCAGTACAGTGACCGGACCAGGCCGGAGTTCTACCTGAATTCCCACATGGACCAGCAGGGTGTCATCAGCGCCATCCGCAGGCTGACACTGCTGGGCGGCCCAACCCCCAACACAGGGGCGGCACTGGAGTTCGTGTTAAGGAACATTCTGACCAGTTCTACTGGGAGCAGGATAGCAGAAGGTGTTCCTCAGCTCCTGATTGTCCTCACAGCAGAGCCATCAGGGGATGACGTGCGAGGCCCTTCAGTAGTCCTGAAGCAGGGCGGGGCTGTGCCCATTGGCATTGGCATTGGGAATGCTGACATCTCTGAAATGCAGACCATCTCCTTCATCCCTGACTTTGCTGTGGCCATCCCCACCTTCCGGGAGCTTGGGACGATACAGCAGGTCATCTCTGAGAGGGTGATCCAGCTTAATCGTGAGGAGCTGAGCTCGTTGAAACCCATTTTGACGCCCTCAACAGGTGCAG
Seq A exon
GTGAGGGATTGGGAGTGGATTCTTTTAGTTAGCTACTTGCTTGCACTGTGTGGTACAAAGAAAGCACTTTCAGGCTTGTTTCCTCTGCCACATAGCATGTGTGGAAAAACTAGGAACATTTTTGTTTTGTTTTGTTTTGTTTTTGGCGATGTCAAGCAATAAAGTTAAGATTCATGTCTGTGGTCAACTTAAAGCATCCAAGAGGGCATGCACATGATGTAGATCCAGGCTCTACAGAGGGGCCTGAGGAGGACCTTTGATGAGTGTCCAACCTAAGTAGCAAGCAGTGGCCTCCTGTTGCCTGGAGGAACTTAATCACAGGTGCTCTGCCCTGACAAGAGGAATGGAGCCTCTGAAATGTTTTTATCTGTAGCACCCGTGTGTGACATTTGCTTGAAACTTGTTCATAAGTCTGAACAAGGTCTGAGCTCAGGAAAGAGACCAAGATGCTCTCACCCACAGTGCAAGCCGGCCCAGGGCTGTGCCTCCTTCCTGGACACTCAGGGCTGAAGGAGACAGACATCACTCAGTGTTTTCATGAGAGGGGACATGAGGGAGTAGGGCAAGGAAGGCAGGGAGTAATATACGTTAGAGAAAGTCAGAGGCAGGATTTGTACAGTGGATTTGCACACCCTTGAGGGGTCAGCTTCCCCCTGGTGTTCGGGAGTGAGCAGTATGCTCTTTATACTTACATGGAGTGACTTAGGATGTTCACACTCACGTACATTTGCGGGGGAAGTCTCTGTCTCTCTGTCCCTGTCTCTCTCTGTGTGTGTCTGTCACTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGACATAGAGGACCACAGCCATTCCCAAACCCCGTTGCACCACAGGAGTGTCTGTTATGATGCACCTCACGGCCTAGGGCTCCTGTATGTGTGGGTGCATGTGTGCATGCTCACAGAACCCCCTTCTTGTGAATCCAGACATATGCTTCCACAGTGCTTGCTTCCATTCACTCTCCCACACATCACACGTCAGAGCGGCCACTCGGTGCACACTCCCCTCCTCCTTCCCATCAAGCTCCCTCCACCCTCATCTCCCCGTGCCTTGCTGCAGACCTGAGTTCCACTTCCTAGAGAACGTTCAGAAGCTTCGCTGGGTCCCTTCTGGTGATGGTTTATCTTCTCAGAGCGTTCTCTTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCCCTTCCCTTCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTCCCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCTTTTCTTTTCTTTCTCCTGGGAGGGCCTGTCTCTACTTCTGCCCTTCCCTTTGAACTTGCTCAGCACACCCTCTTCATGTCTCATTTGCCCTGTCCCCGTCATTCCTGTTCCATTCTCCCCTGTTCTGGATGATTCGTCTCGTGATAAGTGTGCATTGCTCAGACCGGGTCTCTCAGTGCCCTACAGAAGAGCCTGCACCACTTACATGTGCTCTGCTCAGAGTCTCTCCTTCCGTGCAATTCATTGCTCACCCTTCCTCAGAAAGTGCTTTCTCCAGAGTCCCGTGGCTGTCTCTGGACAGTGCTGAGCCAGTGGGCAGTTCCTGCCATAGTTGATACCTGCTTCCTAAAACATCATCGCCAGTCTGATGTAGGCACAACTCTTTGGTTTCTCCATCCCTTGGGCTCACCTTTCTATGCCTCTTGCTGGTTCTTCTTTTGTCTGGTGCTCAGATGTGGAAATACACAAGACTTGCTTCTTTGCTTGATGTTTTCCCTATAGCGTCTGATACTAGAATCTCTCACTTATGGGACACAGATCCGATGACAGACTAGGAAGTGGTTCAAGGGTGACTGGGGTCTGGCACCCTTGAAGCTGAAGCTATGGTCATGTCTGCTTTTCAG
Seq C2 exon
GTGTTGGCAGCAAGAAAGATGTGGTCTTTCTCATCGATGGATCCCGAAATGCTGGCCCTGAGTTCCAGTACATCCGTACCCTGATTGAGAGGATAGTCGAGTACCTGGACATAGGCTTTGACACCACCCGGGTAGCCGTCATCCAGTTCAGTGAGGACTCCAAGATGGAGTTTCCTCTGAATGCCCACTTCAGCAAGGATGAAGTACAGAACGCTGTGCGCAGGCTGCGGCCCAAGGGTGGGAGTCAGGTCTACATCGGAAATGCCCTGGAGTACGTGCTGAAGAACATCTTCCAGAGGCCACTGGGGAGCCGGATAGAAGAGGGCGTTCCGCAGTTCCTAGTCCTCATTTCGTCTGGAAAGTCTGATGATGAGGTGGACGACTCAGCCGTGGAACTCAAGCAGTTCGGTGTGGCCCCTCTCACCATAGCCAGACACACAGACCAAGAGGAGCTGGTGAAGATCTCCCTAAGTCCTGAGTACGTGTACTCCGTGAGCACCTTCAGGGAGCTGCCCAGACTGGAGCAGAAGCTGCTGACGCCCATCACCACTCTAACCTCACAGCAGATCCATCAGATCCTGGCCAGTACCCGATATCCCCCTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000048126:ENSMUST00000097653:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.010 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0009223=VWA=WD(100=86.6)

							
A:
NA

							
C2:
PF0009223=VWA=WD(100=84.7)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000057131





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000115210, ENSMUSP00000137585, ENSMUSP00000140858
  



Associated events






Conservation


Human
(hg38)
chr2:237372338-237374411 
LOW PSI
HsaINT0039511
(COL6A3)
Human
(hg19)
chr2:238280981-238283054 
LOW PSI
HsaINT0039511
(COL6A3)
Rat
(rn6)
chr9:97967535-97969450 
LOW PSI
RnoINT0007852
(AABR07068316.1)
Cow
(bosTau6)
chr3:117460409-117462933 
LOW PSI
BtaINT0042227
(COL6A3)
Chicken
(galGal4)
chr7:4778013-4779053 
LOW PSI
GgaINT0050808
(COL6A3)
Chicken
(galGal3)
chr7:4816347-4817387 
LOW PSI
GgaINT0050808
(COL6A3)
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • 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"