Special

MmuINT0038817 @ mm9

Intron Retention

Gene
ENSMUSG00000027966 | Col11a1
Description
collagen, type XI, alpha 1 [Source:MGI Symbol;Acc:MGI:88446]
Coordinates
chr3:113805453-113808364:+
Coord C1 exon
chr3:113805453-113805536
Coord A exon
chr3:113805537-113808307
Coord C2 exon
chr3:113808308-113808364
Length
2771 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGA
5' ss Score
9.84
3' ss Seq
GATGACTTTTTATCTTCTAGATT
3' ss Score
9.59
Exon sequences
Seq C1 exon
TTCCGCTATGGGGGTGACGGCTCCAAAGGACCAACAATCTCTGCACAGGAAGCCCAAGCTCAGGCGATTCTTCAGCAGGCTCGG
Seq A exon
GTAAGAAAACATGAAGTCATGTTCACACGACCTGATTCTGTACCAGACAGCAGTGTGTAGGCCCATTGAAGAGTGTTTCTATGCATTACATAGATTTTATATGGAAAGACTCTAAAAGCGTATTTATCTTCGAAGTAATAATAGTTACTAATTTAATATTAAATGAATGACCCTTGAATTGCCACATGAAATGCTGACATTATCCCACCATGGCATACAAAGCTCCTATTTTTAAAAGAATATAAAGAGATTATATCTAGGATTCCTTATCTTTCACATCCTGACTTTTCTCTGCTAACTTGTGAACCTATTATTATGGCAGTAATTGTGAAAACACACAATGAAAGGAGTATGTTCCTCTAATTCATAAATGAAATAATTACTTTCATTTTTAGTTAGCTTTAGAGCAGTTAAGATGTAGATGTGAAAATCCAGACAATAAACAAGGAAGGAATCAGAATTCATATAATGCTTTTGTTCATAACTTTATAGTCATTAAGAAAAAAAATAAGTAGGGCTTAGGATTAGTATCATTATTATAACTGTACTGTATCATGTCTAAGATAACTTTTTATTCATGATCATCATTTATGTATCTGTAAAATACTGAATATGTAAATGAAAGTATTAATTTATTTTCTATATTTACTTATTATGAAAAATTATCCATCTGAAAAATGATTATTTGATTGTGTGATATTGAATGATAGTGAGAATATGTGCTTATTATATCAAAGCATATTATAACTAAATTTACTTATAATAACTAATTATCTCTATATTTTTCTTAAAAATTTCATTGTTTTGAATTAGTTGAAGTTAGTACATTTTGAGACTGTAGAATTCCCTGTTTGATTTCTCCTATTTTTAGTCTTTACTGATCAATTATTTCCCTAAAGCATATTTTTAATGTCTTTTGATCAGGTCATCCCCCAGTTCCCTTCCTTCAAATTCTTCATCTAGCTCCATTATCATTTTCTTTTTATTTTCATGTTTTATTTTTCTTTTTTGTTGTTGTAGGTTTGGTTGTAGGTAGGTTATGGTGCAAGGGAGGGGATGCCTCTGTGGGCTCATTCTGAGGCATCCCTTCCCTTTTGGGGAGTTGAGAATGGAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGAGAGAGAGAGAGAGGAGAGAGAGAGAGGAGAGAGAGAGAGAGGAGAGAGAAAGGAGGAGGAGAGGAAGGAAGGAGGGAGGGAGGGAGGGAGAGAAAGAGGGAGAAGAAGAAGAAGAAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGGGAAGGAGGGGAAGGAGGGGAAGGAGGGGAAGGAAGAGGACGAGGAGAAGTCAGCCATGAACAAATGAAGAGAGAGGGTGGAGAGGAATGGGGACAGAAGGGATGGAGAGGGAAGTGAATATGAGGGGAAGAGAGTAGGAAAGTAAGAAAGTAAGAGAGTGAGAGAGTGAGGAGGGTGTGATTAGCCCTTTTCATAGAAAAGCCAGGTATTACCTGGCTGTTGCCAGGTACCTGTGGGACAGAGCCTTAGAAGGAATGATAGGACCATCTCCCTGAGCCTGGGTCAGTCAGGTAGGCCACTTCCCTGATAAAACTTGACAGTGGGAATTCCTGATATCCTTCCAATCCCACGAATCGATTTCGTGTGGCTTGATCTTGTGTAGGTTTTGAGCACACTGTGATAGCATCTCTCAGTTCATATGTACAACTGTCCAGTTGCATCCAGAGTATATTGTCTCATCATAGTCATCTGTCTATCTGGGTCTTAGTATCTTTCTGCCTCTTCTACGTTGATCCCTGATTCAGAAGGCCTGTGCTATGGCTGACTCATTTGCAGCTGAACATTCTGCAGTCCCTCATTCTCCACACATTGTCCAGTTGGGAGGCTCTGATAATCACCTTCTACTGCTAAAAGAAGCTCATACAATGAGGGATGAGAGAGTCACTAATCTACAGTGTAATGATGTCTTTACAGTCAGTTTATATGATTTGTCATGTTAACTTGTTTAAAAGACAGAGAGAGAGATTTTAAATTTCAGTTTTTCAGCTTAATCTCAAGAATTAAGAAGTATGTTGTCCAAACACTCATGGTGAGTTATTGGTGGAACTTCAGAGGTCTTCCTGGTTTTGTTTCATTAATATTTAAAACAGTAAATTAAATTAACATCTATCAAGTATTTTTGCTCTGCTTGGCATTCTAACTTTTCAAATAACCAAATTTCTTATAGTGACTGAATCTAAGGATAAATCATCCAATCAGTCTATTGTGTCCAATTCTGCCTTGTTGCCTCACAATGATCACCATAATTTTTTTCCAAAAAACTACTAGAAAATATTTATCTTTAATTGTTCACCTTAATAAAAGATCTCTACCCAAGATCATGCCTGCACAATGAAGACCAAGAACGTTCTGTTTTTTTGAAGTATGCTTCAGAGTAGAAAATAATTAGATAATCTATTTTTCCTGACATCTATTTTTATCTGATTAAATTTTGGCACTATACTGTACAAGACTGTACAACAGTTTGAGACATGACCGACCAGTAAATAGAACATTCTAGCTATGTGCACTTCACCACTGACTAAACTTTTCCTAGCAAGTTGCTATTACACCTTCCTCAGTTATATATACTACCCAAGGATATCATGTCCAAATGATTGGTGCTACAACATACTACTAGGAAAGAGTTACTAAACTTGATGACTTTTTATCTTCTAG
Seq C2 exon
ATTGCTCTGAGAGGCCCTCCTGGCCCAATGGGTCTTACTGGAAGACCAGGTCCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027966-Col11a1:NM_007729:13
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=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0139113=Collagen=PU(25.4=84.2)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000089793





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000029586, ENSMUSP00000089793f2215A, ENSMUSP00000089793f2216A, ENSMUSP00000121027
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:103012470-103014510 
ALTERNATIVE
HsaINT0037883
(COL11A1)
Human
(hg19)
chr1:103478026-103480066 
ALTERNATIVE
HsaINT0037883
(COL11A1)
Rat
(rn6)
chr2:216938990-216941773 
LOW PSI
RnoINT0038800
(Col11a1)
Cow
(bosTau6)
chr3:40540396-40542450 
LOW PSI
BtaINT0040704
(COL11A1)
Chicken
(galGal4)
chr8:10212685-10212951 
LOW PSI
GgaINT0039309
(COL11A1)
Chicken
(galGal3)
chr8:11949743-11950009 
LOW PSI
GgaINT0039309
(COL11A1)
Zebrafish
(danRer10)
chr24:28762036-28762383 
LOW PSI
DreINT0048847
(col11a1a)
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"