Special

MmuINT0039003 @ mm10

Intron Retention

Gene
ENSMUSG00000032332 | Col12a1
Description
collagen, type XII, alpha 1 [Source:MGI Symbol;Acc:MGI:88448]
Coordinates
chr9:79598991-79602370:-
Coord C1 exon
chr9:79602200-79602370
Coord A exon
chr9:79601180-79602199
Coord C2 exon
chr9:79598991-79601179
Length
1020 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
TCATCTTTGACCTGTTTCAGGTT
3' ss Score
9.34
Exon sequences
Seq C1 exon
GTCCACAAGGCGAATCCCGAACGGGTCCACCAGGGTCTACAGGTTCAAGAGGCCCTCCTGGTCCCCCTGGTCGTCCAGGAAACTCAGGTATCCGAGGCCCTCCAGGTCCTCCTGGATATTGTGATTCATCCCAGTGTGCCAGCATCCCGTACAATGGGCAAGGCTATCCAG
Seq A exon
GTATGTTGCTGCCATCATAAGGACTCCAGTTTCCCAGAAATAAAGAGCCCTAGGATTGAAGGCAGGTCGAGATAGGGATCTCGTGGAGATGCCAACATTTTCGGTTCTGTATTTTGAGTATGCGACAGTCTTCTAAAGCACAAAACACTTTCCATAATTAGGATTTAAGTGACCATTTTCCCCTCCTGTATTTCTGGATTTGCCAAACCACACCATTAACTTCTCTACAACTCTTTGGGGAGTTAAATGAATGCTACCAATTCATTAGGTTTCTTTTTTTTTTTTCTTTCCTTTCTTTTTATTTATTATTTTTACCTAAAGGAACAGAGAGACTAAAAAAATGAAATAGTGTTATAGAATGCTGAAAATATATATGAAAATTATTTCTGCAATCCAATCTACATATAATAGCAAACAAAATGCAGACAAGTGAAAGAATTCACTGTCATGCGCCAGCCGTAGAATTGCTGCTTATCAAATCTGTAGCTTAATATTTTTATAGGGCTGTTAGTGAAATTCTAGTGTTGCACAGTTGTAGACTGCAGACGCATCTCATGCCTGACCTTGGGGGATGTGAGAACTGGGGTGTATACTGGTCTGGATAGAAAGACTCTCATGTTATGATCAATGGTTAGTTTTTCATTAGTGCATCCTCATGCATCTTGCAAGTTTAAAAAATGATACTGCTGTTTGATATGGTTTGCTACTAGCAAGTAGTGCATGAGTAGTTGGATATATCAATATCTATATATCTATATATTTATGTGCATAACTATATGTGATCAAAAGTAGTAATGAATCCAAATGCATAATCCCATGTAATCTATTTGCAAGACTATAATTTAATTATTTGTAAAGCAAATTTAAATTATCCCTGCCTTATGGCATTTGTGAACTGAAAATATATGGATATATAAATATACATACTTTAACATTTACATAGATGGATGTGTATATATATATATATATATTTGCATAGTAATTCAACTTTTAAAAACTATCATCTTTGACCTGTTTCAG
Seq C2 exon
GTTCCGGCTAACAAATTTTCTAAGTCTCCAGTGCTGCTTACAGTTTGAAATACATGAGAATCCTGTTTCTGAGATGTTTGCGCACGTGCTTATTAGAAAATGAGTCTGTATGGAAATCTCGCGGCAGATATGGTTAACGAACTGGGTCGGCATCATACAGGAGGGTGGAGACTCCATACTAACTTGAATGACACAAGGGCAGTGGTGTCCGCCTGATGCTTTTCAGCAGTAACGTAGAACACCATCTTTTAAAAAGTTCAAACATAGCCAGGAGGAGCCCTGGTTGTGAAGGAGGCGCCTAATAAGCTACTAACCAACAGAGTCATGCCATGTTGAGACAGACAATTAACCTGGTTGAAGAGAAATGTCCTATGTAAATAATAAACTAATTGTCGCTTGTACACGATCTGAATGTGATCCTGTATACTAAAATTTCGTAACAACTCAACAACCCGCTTCTGCACCAAAGCCTGCTGGCTGCTTGCTCTCTGCAGTGATAACAGAGAATGGATCTGATCCCCTCTTGCTTGTTAGCAGTGTGTCTGAGTTCAGGGCATGTGACTTCTCAGTACTCTCTGTGTGTATTTTTATTTGGGTTTCTTAACTGCAATTTTTCAAACCAAAGTTTAAAATCAACATCCCTTCCTTTTTGGCTATAGTCACAGGTGTTCCTGCCCACTGGCTGTAACTCTGCATGAGACATAGCCATAGGGGACACCGTGGAGTGTACAAAACCTGGCGACATCTCCTTTCACCCCGAGTTCAGTCTCTAGGCTCCAATACTTTTCATGACCTCAGCTCTCCAAGTTATCTGTTGACCTGATAAGTTTGAAGTCATGAACAGTTATTTAGGGATTTGCCAAAAATCCTACCTAGGTATTGTGTTTACAATTCTTTGGCCCAATTTCTGATCCTTCCCAGGTTTTGTGCAATGATTGTGTTTACTGCTGGATCTTTGAGTCCCCCACTCCCCTGTCCAGCACTCCTTATTTGGTCACCAAATTCACTCTGCACACGTGCACATGGAAATAATTGGAACACCGCAATGCAATGCATCTATTTATGGTTGTGAGATTAAGGGTGGAGTGCCCTCACCTCCAGTGATGAGTTAACTTTTGCTGTGCGTGTATACCTTCCAAGTCATGCCATAACTGTAATGTTGAATCGGACAGAGCCTTATGTGCCCGAGGGTGGGGCCTACCTGCCTGAACGAGAGCCCTTCATCGTGCCTGTGGAGCCAGAGAGGACAGCAGAATATGAGGATGACTACGGTGCAGATGAGCCTGACCAGCAGCACCCTGATCACATGCGTTGGCGGCGAGCCCTGCGCCCAGGCCCTGGGCAGTGAACCTGAAATCACGGGTTCACTGAGGTGGGAGGTGCTGGGATTCTCAATCACAGGTCAGACAGAGCAGCAGTGTACGTCATTTCTGTGATGTTTTCTCTGCGTCGCTTCACCCACAAGTGCTCCGATCTGACTGTAGAGAATCTTGTTTCTGCAGGCAGCCTAGCTGGCAACAGTCTGTAGACATCCATGCCTTTGCAGTTCAAATGGTTACAACACAAGCTCTTCACAGAAGCTGCATGGAGAGAACGCGTCCAGGGTGGGCTGCGGCAGCCAAGCTTCTAGGTTACCCAGCAAGCCCTGGAAACCAGAGCAGCTGTCTATTCAGAAAGGGCCTTTATCTTTCTTAGAACAAATGCAGTTCAATTGCATCCCATTTCCAGTCATTCCACTCTTAAAACCAAAAAGGAGGGGAACACCAGCTCACTGCAGCAGTTCTCCCTTCTTTCCTTCCTTCTGTTACGCTTTAGGGCACAGAATGCTCTTTAGTCTTTTAACAACCACAGACCTTAAGCCTCGTAGCCGAAGTTATTGTATCAACTGGATACTGTTCCATATCGCTTTTAGACGTCTTTGTTTTGACACACTAACATTTATGCCAAATTGCAGATTATTCTGCAGAAATGGAATTGCATGTTTGTGTTGTATATTTAGAATGAACTTTTTTTTTTTTTTTTTGCAAAACATGTTTCTTAGTTATCAAAGCAGTTGGAAATGTTTGCAAGACTATGAACATAGAATTGCTGCTTTTATATTTTAACTGCAGATTGTGAATTTCACTGCCTTATATTATTTATTTCTGAAACAAAAGAGGCATTTTTCAATAAAACTACTGAAAATTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032332:ENSMUST00000071750:65
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0139113=Collagen=PD(72.4=72.4)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000112604





     
                   









    
Main Skipping Isoform:
ENSMUSP00000071662





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000123455
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr6:75086558-75087576 
ALTERNATIVE
HsaINT0038011
(COL12A1)
Human
(hg19)
chr6:75796274-75797292 
ALTERNATIVE
HsaINT0038011
(COL12A1)
Rat
(rn6)
chr8:87042979-87044012 
RnoINT0038959
(Col12a1)
Cow
(bosTau6)
chr9:14870819-14871837 
BtaINT0040890
(COL12A1)
Chicken
(galGal4)
chr3:80309501-80310622 
GgaINT0090134
(COL12A1)
Chicken
(galGal3)
chr3:83645803-83646169 
ALTERNATIVE
GgaINT0090134
(COL12A1)
Zebrafish
(danRer10)
chr17:49687038-49689983 
LOW PSI
DreINT0049090
(col12a1a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CCACCAGGGTCTACAGGTTCA

				
R: 
CACCACTGCCCTTGTGTCATT

				
Band lengths: 
352-1372

			

		

	





	
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • 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"