Special

MmuINT0040081 @ mm9

Intron Retention

Gene
ENSMUSG00000067158 | Col4a4
Description
collagen, type IV, alpha 4 [Source:MGI Symbol;Acc:MGI:104687]
Coordinates
chr1:82447298-82450638:-
Coord C1 exon
chr1:82450352-82450638
Coord A exon
chr1:82449970-82450351
Coord C2 exon
chr1:82447298-82449969
Length
382 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TTTATTCCTTGTCTGGGTAGCAC
3' ss Score
6.44
Exon sequences
Seq C1 exon
GTTTGGCAGGCTCTTGTCTTCCTGTGTTTAGCACTCTGCCCTTTGCCTACTGCAACATCCACCAAGTGTGCCACTACGCCCAGAGAAATGACAGGTCCTACTGGCTGTCCAGTGCGGCTCCTCTTCCTATGATGCCACTCTCAGAGGAAGAGATCCGCTCTTACATCAGCCGCTGTGCGGTGTGTGAGGCCCCAGCACAGGCCGTGGCGGTCCACAGTCAGGACCAATCCATCCCACCGTGTCCACGGACATGGAGGAGTCTCTGGATTGGGTACTCATTTCTGATG
Seq A exon
GTGAGTCTCCTGCCCTTGAATCTTATTCCTGTCTAGATAGTAGTACTGGGTAGAAACCAGAAGCTATGAGGCCATGCAAGCTACTGCAGACTATGGACTGGTGAGATTTAGGGCCATCATTATTGCTTTTATCTTTTCTCATCAATTATTCTATTGGTAAGTCTGGTAGAAGATGGATTTATTTCAGCCATCAGTGAAATTGGCTCCATTTGGCACACACACACGACACACTTCCTACTGCTGTTCAGCAGATTGTAAATTGTTCTTTATGGAGTGACTTAAGGAGGGATTTTAGAGTAGAGCCAGACCTGGGCATGCCGCTGGTTCTGTCCTGGTGGTCTTGAGTACCTGAGCTCTAATTCTTTATTCCTTGTCTGGGTAG
Seq C2 exon
CACACTGGAGCTGGGGACCAAGGAGGTGGGCAGGCACTGATGTCACCTGGCAGCTGCCTAGAGGACTTCAGAGCTGCACCGTTCGTTGAATGCCAGGGCCGACAGGGAACCTGTCACTTTTTTGCAAACGAGTACAGCTTCTGGCTGACCACCGTGAACCCAGACCTGCAGTTTGCCTCTGGCCCGTCACCAGACACCTTGAAAGAAGTTCAGGCCCAGCGCCGGAAAATCAGCAGGTGCCAGGTTTGCATGAAGCACAGCTAAAGAATTCAAAACATGCCAACATGCCAACCCGCATCAAGGCAGACATCCAGTGGAAGACAAACTTCCTCAACTATTCCAGCAAATTCAGTGGTGCTCTCTCCAGACTTCTGCCATGCCTTGTTCTCAGCGTGGTTATTCCCGGCCTCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCTATGGATCAAGCAAACACTGTACATGTGGAGTTGCTCCCCCTTCTCCTTTTATTGAGATTATAGAGAACAGACTTTATTTGAACATGTGTTAATTCCCAAAAAAGCAAGCGGATGACAAAGACCAGATTATAAACTTCATTCATTGGTCGATAGAGTCTCAAACAACTGAAGTCAATTATTCTGTAATCTATTGGGCTTCTGGCTAGATTTTATAGGAAAAAAAATATAAATAGGCCAACAAAGGAAGCGATGAAGTAGAGATTTTTCAGTGTTTCAAAATGATTCCCTCTATAATCTTTTTTTTTTTTTAAGCCAGGCACTTTAAATAATTGTGAGACCATGGCCCAAAGAGGTTTTTAAAAAGGAGGAAGAAAAAGAAAACCAACCTTTCTACACTGCCAGCATTAGCAGATCATTTCAAAGCAGAAATGGGTCATTATGCAGGAAGGCCTGCAGTCCTGTATTCCAGAGCCTCGAGATTAGCATAAACACTTCACAGATGAATATAAAACATTATGTTCTCTTCTGCATTTTACAGAGAATGGAAATGCCTACTTTGGCAACCCCTTTGAAAAGTAGCAATTATAGAAGAAATATATTCAATAAGGGATTAGGGGCCTAAAAGCTATTAATGAATATTAAGGTAGTGATTCACAAAAATTGACTCCCCCGTCCCAGGGAACTCGCAAACAGACCACTTTTCCCCAGTCGGGGGCCAGCATGTCCTCCTGCTAATGGGACTGAAGCCACATGGGGCTTGCTCAGGCAAGGGAGAGCCTGATGCAAAGCCACTGGCTTTCCTTCCCAGGAGAAACTGTGAGGCTCCTCCTCCAGATGGATAATGGTGACTCACTCCGGAAGTGACAGGGCTATCATTATGCACTTGGGAGAAAATTAAGGGCTGACTTAATTAAACTTAGGTAAGAAGATTCGTTTATGTCAGGGTCACCCCACCAGGAAAGCATGGGGCTCTCTTGAACAGAAACAAAGACTATAGCCAATCTGAATTTTGTGTCCCTGTGATTTTTTTTTTTTAAATTGGAGAGCATCTGTCTCTCCAATTTTCAAACATTCTTTATATTGTATTAGCATCATGGCAAGACAGTTGTTTGACACTGGTACTTAGCAGCTCCTGTACACGGGTAGGATCTCTGTCAATTTGCAGTGACTTTTCTGCATACCAAAAGGTCTGCTTGCTATCAAGTTGGGGATGCCTACAAACCACAAATTGAAAGGTTTGCTAGGAAAGATTTTTTATTTTTTTTTGAAACTCACCTTCCTCAGCCAAAGTAAAATTGCCATTTTAATGGAAAGGAAGGATTTTTTCCCCACTGAGAGAGACACTCATGTCAGAGCTCACTTTTCAGTGCACTTTAGAATAATTGAAAGAAAAACTCAATTAAAATGTGGTTTCCGAGGCTGGGGGGCAGGGGGGCGACTCGGGCTAACAGCATTTACTGCTTTTTCAGAGGAGGATCTGAATTCAGTTCCTGGCACCCAGGAACTGGCTCCCAGTCACCAGGAACTCCAGTCCCCCTTTCTGGCTCCTAGGGGCCCTTCTGTACCCATGCAAACGCCCACCCACAGACATACTCATACACATAGAAACAAAAGTAAATAATGATACTTCTAAAGAGTGTTTGCCTTGCCATCATTTGGCCAATGATGAATTCCTTCATGCAGAATACATTTAGCATTTTTATCTCTGTAGGATGTCTATGGGATGGCATTTTAAGATAAGTTTCTGGTAAATAACATTTTATTTTATTATGTTTTAAGATAGCACCCCAGTCTATAGTTCAAGTTGGCCTGAAACTTGCTACACAACCTCACATTGGCTTCAATATCCTGGCAATTGCCTGGCGTCCCAGAAGTGTTAGAAGCCCAGCCTTTAAAAAAAAAAAAAAAAAAACACGGTTTTTGTTTTGCTTTGAAGACGTTGTCTCTGCTTGGTCTGGAACTTGCTATATAACCAGGGCCAAACATCTCTATTTTAACATAAGATATTTTCTCGATGTAACAGAAGTTTTTCTATTGACCCATTTGATTCTAAGTTCAATGCTGTGCATGTTAAATATTTTTTGAGTGTCCATTTCTCCTTTATTTACATTACTCTTACGTTTCCAGATTCTACATTTATCATTCTAAACCAGGCCTGAACTTGGCCTGAGAACATGTTCCCGGAAGAGGTGGTTGGGAATA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000067158-Col4a4:NM_007735:47
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=0.080
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(25.6=31.2)

							
A:
NA

							
C2:
PF0141314=C4=PD(72.6=96.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000084253





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000084282
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:227007589-227008017 
ALTERNATIVE
HsaINT0039123
(COL4A4)
Human
(hg19)
chr2:227872305-227872733 
ALTERNATIVE
HsaINT0039123
(COL4A4)
Rat
(rn6)
chr9:88237551-88237929 
Cow
(bosTau6)
chr2:115971382-115972454 
LOW PSI
BtaINT0041847
(COL4A4)
Chicken
(galGal4)
chr9:8789626-8790422 
LOW PSI
GgaINT0032163
(COL4A4)
Chicken
(galGal3)
chr9:10382473-10383269 
LOW PSI
GgaINT0032163
(COL4A4)
Zebrafish
(danRer10)
chr7:50648682-50650357 
LOW PSI
DreINT0049897
(col4a6)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GATCCGCTCTTACATCAGCCG

				
R: 
GCTGGGCCTGAACTTCTTTCA

				
Band lengths: 
356-738

			

		

	





	
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"