Special

MmuINT0040174 @ mm9

Intron Retention

Gene
ENSMUSG00000031273 | Col4a6
Description
collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695]
Coordinates
chrX:137604102-137606769:-
Coord C1 exon
chrX:137606653-137606769
Coord A exon
chrX:137604294-137606652
Coord C2 exon
chrX:137604102-137604293
Length
2359 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGG
5' ss Score
6.23
3' ss Seq
TTATGTCCTTTTCTTCTCAGGAG
3' ss Score
9.37
Exon sequences
Seq C1 exon
GTTCCAAAGGCCTACCTGGCATCCCTGGTAAGGATGGCCCCAGTGGGCTTCCAGGCCCATCTGGAATCCTTGGTGATCCTGGTCTCCCTGGACTACAAGGACCTCCAGGATTTGAAG
Seq A exon
GTCAGGTTAACAAAACTTGGACACTTAGTCAACCATGTGGTAAATTTGCCACTATGAGGTCGCTCACAGGCTGAGTTCTTGTCTCTCTTTATGTTCTATTACTATGAAGAGACACCATGACCAAGGCAACTCTTATGAAAGAAAGCATACCAGGATTGGAGTATTGCTGTGACAGGCATGATCATGCCTTTGTTGAAGGAATATAGAAGACTTTGGGACTTTGGACTAGAAAAGTGATTGGATACATTAAGTAGGGTGTAATGAGCCATAATAACAGGAACAGGGAAGATAGTATTAAGGGCAATTTGAACTTTAGGGGCCTGGCTGAAGAAGTTCCAGGGGGAAATAATATTAGTAAGTAGGCTAGATACCATTCTTGTGATATTTGGCAAAGACTGTGGCTGCTTTTTGCCCTTCCCATAAAAATCTGCCTGAAACTAAACTGAAGAGTTTTGGATTAATGAGGTTCGCAGAGGAAATTTCAAGATAGCCTAGTACTGACTGTGCTGTGTGGGTTTGATAGCGCTTATACAGATCCACAATGAAAAGGAGCAGGGGAAGCAAGGGGAAAAAAACAAAATTTACAGTTTGACGAGAAAAGGAGTACCAGTAAATGTTTTGTTGGAGCCAATTCTAGTGCTCAAGAAGATAAAAAAAAAATTTTTTTAATCCTGCTGCTAAATGAAATAAAAGAAGTAACATCAGGGCAAGACCCCACTTCTGGCACAATCTTATGTCTTTCTCACTGTTCTATTCCTGTGAAGAGACACCATGACAAAGGCAACTCTGAATAAAAGAAATTATTTAATTGGGGGCTTTCTTGTAGTTACAGAGGTTTAGTCCATTATCATCCTGAATGGAACATGGCAGTAGACAGGTAGGCACTGGAGCAGTAGCTGAGAGAGATACTTCCTGATCCATAGGAAGACAGATATACAGACACACATACACACATACACACATACACACAAACACACACACACACACACACACACACACACAGAGAGAGAGAGAGAGAGAGAGAGACCCTAAGTTGGGCGTGAGCTTTTGAAACCTCCAAGCCTATCCCCAGTGACACTTCCTCCAACAAGGCCATACTTCCTAATCCTTCTCAAATAGTGACATTCCTGGTGACTAAGTGTCTTAGTTAGGGTTTTCCTGCTGTGAACAGACACCATGACCACGGCAACTCCTGTAAGGACAACATTTAATTGGGACTGGCTTACAGGTTCAGAGGTTCACTCCAACATTGTCTAGGCAAGAGCATGGAGGCATCCAGGCAGGCATGGTGCAGGAGGAGCCGAGAGTACTACATCATCATCTGAAGGCTCCTAGCATAATACTGGTTTCCAGGCAGCTAGGATGAGGGTCTTAAAGCTCATACCCAACAGGGCCACACCTTCTAATAGCACCACACCCTGAGCCGAGCACATACAAACCATCATATTAAGCATTTAGCTATATGAGCTTATCACAGTCTTTCTTATTCAAACCATCACATTGTTCTTCTCTTCACACTGCACAGGCTCCAGCCTATGATGAGAAGTCCTTCATACTTCAGTAAGGCAACAGACTTCTCCTCCTTGTCTGGGCTCTCCTCCAGCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTACCTACCTACCTACCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTACCTACCTACCTACCTATCTATCTATCCCAGTATCTTGCTGCAAGCCCAGTTTGCCCTCAAAGTCACTATGTAAGCCAAGTTGGCTTCAAACTCTTGATCTTCTGCCTTTGCTTCCCATGGCTTTCTGTCCTGTCCTGACATGGATGAAAGAATACAACAAATTACTTGTCCTTGGTATAGAATCCTTCTAAAGCTCAGTAGTAAAATATTGAAGTACAGTGGTCATATCCACCATGGACAAGAGAGGCAGATGCAACTTTGCCCTTCTAATGCTAACGTTACTTATAATGCTTCTGATTCAGCAGCTAGTTATGTCCTGTGAGAGACGCCAAGGGTGGGGATGAGAAGGATTCCACTCCATTTACTCTTAGAACCGAAGGCCGGGAGGCTGAAGAAGGGGAATGGATAGTGTACTCTTTTAAAATGGGAAATATTTAGCTGGGCACACACATGACTTGGAGTTGTAACTCCATTAGCTTCTAGCTGTGGCAGCTCAGAACCTCATTTTCCTCAACTGTAGAACAGGGGGTATCAGGATCAAGTGTTTGAACACACGCATATGATGCGCCTTACAAATGTTTAGGATCAATGAGTGGGTAGTGTTATTACCATCTGCAGCATGCTGACTTTTATGTCCTTTTCTTCTCAG
Seq C2 exon
GAGCTCCGGGAAATCAGGGCCCCATTGGGCAGCCTGGGATGCCTGGGCACGGTGTGAGAGTGGGCTACACACTAGTAAAACACAGTCAGTCAGAACAGGTGCCACTATGCCCCACTGGGATGAGCCGGCTCTGGGTGGGTTACAGCTTGCTCTTCGTGGAGGGGCAGGAGAAAGCCCATAACCAGGATCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031273-Col4a6:NM_053185:42
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=0.338
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0139113=Collagen=PD(44.1=65.0),PF0139113=Collagen=PU(61.0=90.0)

							
A:
NA

							
C2:
PF0139113=Collagen=PD(37.3=33.8),PF0141314=C4=PU(39.8=66.2)

						

					

				








    
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:108160655-108161618 
LOW PSI
HsaINT0039216
(COL4A6)
Human
(hg19)
chrX:107403885-107404848 
LOW PSI
HsaINT0039216
(COL4A6)
Rat
(rn6)
chrX:112408837-112410979 
RnoINT0039941
(Col4a6)
Cow
(bosTau6)
chrX:61057113-61057989 
LOW PSI
BtaINT0041933
(COL4A6)
Chicken
(galGal4)
chr4:14057642-14058349 
ALTERNATIVE
GgaINT1010115
(COL4A6)
Chicken
(galGal3)
chr4:14208044-14208751 
GgaINT0073167
(COL4A6)
Zebrafish
(danRer10)
chr7:50651095-50651673 
LOW PSI
DreINT0049895
(col4a6)
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"