Special

MmuINT0040494 @ mm9

Intron Retention

Gene
ENSMUSG00000043719 | Col6a6
Description
collagen, type VI, alpha 6 [Source:MGI Symbol;Acc:MGI:2444259]
Coordinates
chr9:105688009-105691322:-
Coord C1 exon
chr9:105691225-105691322
Coord A exon
chr9:105688606-105691224
Coord C2 exon
chr9:105688009-105688605
Length
2619 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
TGTTATGATTGATTCTATAGGCC
3' ss Score
7.4
Exon sequences
Seq C1 exon
CTTTCAGGTTGGGGATTCCTCAGCCTACAACCTGAAAATGCTGCTGGTTTTGTGCCTGACAATGATTTGTTTCCACGTGTGTGTGAACCAAGATTCTG
Seq A exon
GTAAGAAGAAACGGAAGCTCTTCCTTTTCATAATCCTTCTTATACTCACTAGCTAGCGAACGAGTGTAAGCTGCTGACATTAGGGCGGTTGCTTCACTTTCAGTGCCAGTGAGGATGTGGGGACAAAGTTTTATCTTTTTTTGGTTACCCTGCATTCCTTGGAAATCCTGGGCTACTGATAAAATATAAGAACACAATCCTTTTGTCCTCAATTCAACCCATTCTGGGATTCCTTGGGAATTCTGTTAGGTTAAGCACTGGAAAATTCAGAACGTCTCTGTTTTTAATTGACTTGACTAAAAATGTTGCTTTAGCTAAATGTGTGGATTTGCTGCCTGCTGCTGCAGCTTGTTTGACGTATGCTTATAAAAGCATGCCTGTGTTTACCCCGGAGAGAGCTCCTAGCTGTCACTGACAGTAATTGTGGTCAGTAACTCATGTCCAGTAAAATGAAGTTCAAAACACCCTCCACTGCCTCCTCTAGCCCTGCTTAAGGAGTTGGTATAGGTGCTGGCCGGCTCAGGTCCAGGACTACCTACACTGACTTTATAGCTTCCTCTAGGATTCTAATCTTGAAACAAGTTTTGTGGAGATAAACTAGACTTTGCCCCCAAAATATCATCTGCTGTCTCTCTGAGCCTTAAGCTTTTTAAGAAGAGTCAATCTCCACTCCTGCACACACACACACACACACACACACACACACACACACACACGCGCATACACACACACACACATACACACACATACACACACACACACACACACACACACACATTTCATGGCTTAGACTTGATAAAGGACCTGGACTATCTCACTGATAATCAACCACGTGTCTTTCCTACACAAGATGTAGGCGTGTACGCAGGAGGAGAAAGGTCACTATGGCCATATAACAACCCTCCCTGAGCAGGGTTCGCTGGACCAGCCAGCCTTCCCTTGGAAGAAGGTCCTACTGGCCCTCCGCTCATTCTTCCCCTGAATGCTTCTGTAATCAAGTCAAGAGTCTCAGACTGCTGCGGATGAGGTCACTCGAAAGATGAGAAAGAACCAATTTATCCTTCGAGCTCTGGTCAGATGCTCCTAGAGACCGAATGATGGAAGCCAGGCCTGCTTTCTTAGCAACAGCAGAAAAAGAAAAAAGAAAAAACAAAAACAAACCAACCAAATAAAACAACAACAACAACAACAAACCCAGGAGCTAATAGGACTTGATAGGGATTTATCTAGTAATCATTTGTAATAAGAGGAAGTGAGGAGATAGCCTGGGTATTTGCTAATTGAACCTACATGTTTTTAAAGCAGGGGAGACTGGGGCTAATGTATGTTGGATAACTTAATAAAGCTCATAGAAAAAGCTGATGACAGGCAGGCTTCCTATCATATAATCCAACTGCACTGCATTTTCTCAGATAACACACACACAAGCACGTGCCACTTACCTGTCTTCCTTGATGATAAAGTGCTGAAAGCTCACAGACCAGACAAAAAGCTGTCAGTAAGAGAAACTAGTTTAGACTATGATTTTCTATAAGGTAAAAAAATAGAATTGCAGAGCCTAGCATGGTGATAGGAACATGCCCGTAATTCTAGCACTTGGGAAGTGATGGCAGGAGATCAAGAGTTCAAAGCCAGCCTGGCAAACATGAGACTATGTCATTCTTTTATTCATTCATACACACACACACACACATATATATATATATGAAAGGCCAATTCCAAGTCCTCCTCCATCAATAAGCAATCAAGGAAAGGCTCCAGAGACATGCCCTCAGCTTGCAAATTAATTGTTTAAAGTTCAGAAAGGTTTTTGTGTTCCAACATAAAATATGCTTTAATAGAAACTAAGATTGTAATCCTATTTCTCACTTCAAGTTGTTTGCTACCATCATATCTTGTGTATGAGAAGATAAATTTATCAAACATGATACTCATTCATATAACATTCTGAATGTATTAGAAATAACTTTCCTGCAGACTAAGCCAATCCTGTGCATTCATGATGTCTCAAGCTTCATTAACTCAACACTTTGTAATACAAAAATAATGTTTGCAAATTCATCAGATAACCTGAGGCATCACTTAAGTGAGAATCACAGTGAAAGACACTCAGGTTTCAGAGTTCTAATCAATGTGATGGTGTCTGATTCAAATGAACATGTTCAATGTTTTGATGTATGTATGTATGTGTGGGTATATGCATGTGTGTGTGTGTGCACATGTGTGCATGTGCCCACCTCTAAAATTCCATAGGGAATACAGGAGGAAATTGCCCAGTAAAGAATAAACTGCTTTTTTATTTTTTGCTGTTTTGTTTTGATAAGTTTACCTATTCCCAGTTAGCTAATTGCTTGCAAAATGTGCTCATGGTTGCAAAGCTTTCAAATGAGAAGCTGTCTAAAGCACACACATCAAGAAACAAACTCTCCTTTTCCTGAGCGATTATATATGGTGTTACACTATCCTGTTTAATTTGTCAGGAAGGTAATAAATTTTTTTCTCAAAGAAAACACTAACTTTCTCTGTGTGTGTCTGTGTGTGTCTCTCTGTGTGTGTGGTTGGCATTAAACATGGCAGAAAATGTATAAAACTTTCGCTGTGTTATGATTGATTCTATAG
Seq C2 exon
GCCCCGAGTACGCAGACGTGGTGTTTCTGGTGGACAGCTCCGATCACCTAGGGCTTAAGTCCTTTCCTCTTGTGAAAACTTTCATCCACAAGATGATCAGCAGCCTCCCCATAGAGGCCAACAAGTACCGCGTGGCCCTGGCCCAGTACAGCGATGCTCTCCACAATGAGTTCCAGCTGGGCACCTTCAAGAACAGGAACCCCATGCTGAACCACCTGAAGAAGAACTTCGGGTTCATCGGTGGCTCCCTGAAGATAGGGAACGCCCTGCAGGAGGCTCACAGGACCTATTTCTCTGCTCCCACAAATGGAAGAGACAAGAAACAGTTCCCCCCAATCCTGGTGGTGCTGGCTTCAGCAGAGTCTGAGGATGATGTGGAAGAGGCTGCGAAGGCCCTGCGGGAAGATGGGGTGAAAATCATCTCTGTGGGGGTGCAGAAGGCTTCTGAGGAAAACCTGAAGGCGATGGCCACCTCTCAGTTCCATTTCAATCTCAGGACTGCCAGAGACCTCAGCGTGTTTGCCCCAAACATGACAGAGATCATCAAGGATGTGACTCAGTACAGGGAAGGAATGGCAGATGACATTATTGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043719-Col6a6:NM_172927:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.035
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0009223=VWA=WD(100=89.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000096040





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000060840, ENSMUSP00000125765
  



Associated events






Conservation


Human
(hg38)
chr3:130560429-130563067 
LOW PSI
HsaINT0039583
(COL6A6)
Human
(hg19)
chr3:130279273-130281911 
LOW PSI
HsaINT0039583
(COL6A6)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr1:153435960-153438272 
LOW PSI
BtaINT0042229
(COL6A6)
Chicken
(galGal4)
chr2:42140015-42140060 
GgaINT0095477
([1])
Chicken
(galGal3)
chr2:41559508-41559962 
GgaINT0095477
([2])
Zebrafish
(danRer10)
chr17:49860518-49863570 
LOW PSI
DreINT0049075
(col12a1a)
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"