Special

MmuINT0040176 @ mm9

Intron Retention

Gene
ENSMUSG00000031273 | Col4a6
Description
collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695]
Coordinates
chrX:137599946-137603423:-
Coord C1 exon
chrX:137603137-137603423
Coord A exon
chrX:137601522-137603136
Coord C2 exon
chrX:137599946-137601521
Length
1615 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
ACCCCTCCCTTCTGTTTCAGCAC
3' ss Score
11.97
Exon sequences
Seq C1 exon
GATTTGCTGGCTCCTGCCTGCCCCGATTCAGCACCATGCCCTTCATATACTGCAACATCAATGAAGTGTGCCACTATGCCAGACGCAATGATAAATCTTACTGGCTCTCCACTACTGCCCCCATTCCCATGATGCCTGTGGGCCAGACCCAGATTCCCCAGTATATCAGCCGCTGCTCTGTATGTGAGGCACCCTCACAAGCCATTGCTGTACACAGTCAGGACATCATTGTCCCACAGTGCCCTCTGGGCTGGCACAGCCTCTGGATCGGATACTCCTTCCTCATG
Seq A exon
GTGAGGCCTTGAACCATTCTGTCCCTCAATGGAGAAACAGAGATATATAGGGTAGGGGTGAAGAGCTCAGGAAAGGACCCTTCCTTTGATCCCAGGCTCAAGGGGACAAAGGATAGAAAATAGTTTAACAGGAAGAGAGATGAAGATGGGAATTACAATTTTGTGGTTTGCAGGGTAGAAGGTGGGGTTAGATAGCAATTTGAACCTGGTGTTCTGGACTGAGAACCTGTATGTGTCACAAGTCAAGGCCCTACTCTATGTGTCCTTCAGTTTTCTCACTACGAAGGGAACACTAGAACTGTAATCTGAACAGATACTGAGAGAAATACTGTCCTCAACAGAGGCCAACACGTAATTGTACTGATCAGGCTGAGAAGAATATTTACCACCTTGCAGTCTGCCCTCCCAGATCTGTCTAGCTTCTACTATCTCTTTTTGATATCTCCTCTTAAAGATTGGCAAGGAGGCATGCTGCGTTTGTATGGCCTTCATTGCTTCTCCAGTTTTTGTGGTGTGAAGGCATGCTGTGTATCTAGCTAGGAAAGAGAACATCAGTAGTACCGAGGAGATGGTCCCATAACTATCTGGGGAGGTTTTTTCAAATGAAATCAGGAGTAAGACTAAGGCAACTCCCAGGAAAACTACAGTGTAAAGCTCACTGAAGTCCCCTGGTTGGGCAGAGCTTCTCACTGAATCACCAAAGACTCTGGTACAACAGCTCCCACCCAAAACTGACATGTTTTCGTAAGCCAGAGCCATCAGCAAAGTATCACTCTCTGAAAGTTAAGCAAACTGACAGCCTGCTAGCCACTTGCTGATGCAGATTGCATAAAGCCTCCTCTTGGCCTCCTGTGCTTCCAGCTAATCTGAAGGGAGATGGCTGGAGTATAGACAGGAGGTCTGGAGGTCTAGTGACTAGAGACTGCCAGAACAACTGTGGCCTAGAAACTGAACTCCAAGTAAGCCCTCTGAAGTGAGGCCTGAGACATTTTAGGTCCTTTGTCAGGTAACAAATATTGTGTGTCACTCTAGAGGGTATGGCACAGGTTGAAAATAGAAATAGTTCTAGTAGAGGCAGTCTTAAGGATGAGAACTATAGGGGACATGCTGTTACAAGAAAGAGCATTGGGGACTACTATATGCTTTTCCTTCTTAGAAGACAGTGCCCAGCAATGGGCTTAAAGCTTTGTTAATTCCACAACCTAAATCCAACATTGTTCCGGTGTATATGTCTGAGGACCAAGAAGATGGACCCCTAGGAAAAGGCATTTACCATACACACACACACACACACACACACACACACACACACACACACACACACACCTGTGGAAATGGGGAGCTGAAGGTAAACCTCACACAGCTGTGAAGTCCGAGGGAAACATTGGTTGGAATGGGATCACTGATCACGGAGGTCCCAAAGGAGCTGCTTAGAGAGGATGGCCAGTACTTGCCTCCGAAGCCCAGGTTCATCAGGCAGGCTAGAAACTGAGTGATCTGGAGGGGTCCAGAGTTCTAGAATGGTGCACATATGAAGTCCTGTAGAAACAGGCCATGGAGCATCTCTGTGTTGACTTCTGGCAGAGCTCACACAGACCCCTCCCTTCTGTTTCAG
Seq C2 exon
CACACTGCTGCTGGGGCTGAGGGTGGAGGCCAGTCCCTAGTCTCCCCTGGCTCGTGTCTTGAGGACTTCCGGGCCACTCCTTTCATTGAGTGCAGCGGCGCCCGTGGTACATGCCACTACTTTGCCAACAAGTACAGTTTCTGGCTGACAACGGTGGAGGAGAGAGGGCAGTTTCGGGAAGAGCCCGTGTCTGAGACGCTGAAAACTGGGCAGCTTCACACCAGGGTGAGCCGCTGCCAGGTGTGTATGAAAACCCCGTAGGGTACTGCCCGTCATCCAGCCCACCTCACAACACTCACCTCAACAGTCTGAGAAAGGAAGGCCTGAGCCCATCTGCCTGTCAAGTTGTACATCAATGCCTCGTTTGGACTGGACTACTGGACAATGGTCATCCCAACCCTCAGACCCAACAGATGAGCCCACTGTGCTAGGATTTGCTTTCCTGTTTCCATCCATCTGGTGCTAACATTCCATTTAGATATGTGTGTGATTACTCATGGCTACCTTAGGAAGGTGTGCTAAGCTGTCACTTGCGAAGATGGCTAGAGCTCTCTTCACTGCCTTAAGCTGGAAGTTCTTTATAACAGCGAAGTTATGTCTTTATGACAAGACGTCACCACACATCATTTGAGTCAAACTAAAGCTCAGGATTTCCACCCTAAAAATACGTTTCTGGCTGAATATGATAGATAATTCAAGTCTGCCTAGGGCTAGCCCTCCCTACTGAAGGCAGCCTATTATATTTAGACAGGCAGTAGTGTTGGAATGAGAAACCAGCCTATAGCCAGAACTGAGCTGTGATTCCTTGCAGAGTTTTGTTAAGCCCATGCCCCATCTTGAGTAGGAAAGGCTGAAAGGCCAGTATTTGGTCCTAGACAAATCACTGTCCCCTGGTCCCACATCTAGAGATATAAGACAAGTTGGCCCAGTCCAAAGTGGAACCAAGAATTCGATAAGTGTGATCAAGCTTGTCACAGAAAGACATGAGAATCACTTCTCCTTCTTCTTGGCCTAGGGCAGAAGGAGAAATACATATAGAGGTAGCAGTTTTGCTTCTGAGTCCAGGAACCAAAAGGTAAAGCTCATGTCCCCATTCCTCAGAAGTCCCTAGTTATTCCAAATGCCACCCAGATTTATGCAGGGTGACAAACTGAAGCTGCAGTGTGTTGGCTCCTTGCATGCTGAGGCTCTTAGAGGTGTTCTGATAAAATGGCCATCCAAACACCCTCCCACGGGTAGCCTTTTAAACTATTTGACAGGGTTTTTTTTTTTTAATTTCATAAAAATCTAGCACACACCAATGTTAGCAGACCCGAGGTACATTCTGAGCTGGCCATGAAGTATACTGCCTTCTGTTTGAAGCAGTTCATTTTAATTACCAGTTGCGGAGAACACAATCAGTTCCACTGACATGAAGCGCTCCCTTGCAGGTGATTGGCTTCCTTGAGTACTATGTAAACCGTGCCCACGCAGGCAAAGCATAACAAGTACATTCTGAGCTCTTGTTATCACCTCCTAGATAAGTAACAAATGGTGTCAGCTTTGTACATAGCAAATAAAATTAATGAAATACGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031273-Col4a6:NM_053185:44
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.058
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(25.9=31.2)

							
A:
NA

							
C2:
PF0141314=C4=PD(72.4=96.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000098765





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000098765f2812A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chrX:108157261-108159461 
LOW PSI
HsaINT0039218
(COL4A6)
Human
(hg19)
chrX:107400491-107402691 
LOW PSI
HsaINT0039218
(COL4A6)
Rat
(rn6)
chrX:112405910-112407632 
Cow
(bosTau6)
chrX:61054655-61055342 
LOW PSI
BtaINT0041936
(COL4A6)
Chicken
(galGal4)
chr4:14059058-14059679 
LOW PSI
GgaINT1010117
(COL4A6)
Chicken
(galGal3)
chr1:143303033-143303284 
GgaINT0073169
(COL4A6)
Zebrafish
(danRer10)
chr7:50648682-50650357 
LOW PSI
DreINT0049897
(col4a6)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TACTGGCTCTCCACTACTGCC

				
R: 
CCGTTGTCAGCCAGAAACTGT

				
Band lengths: 
343-1958

			

		

	





	
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"