Special

MmuINT0039032 @ mm9

Intron Retention

Gene
ENSMUSG00000058806 | Col13a1
Description
collagen, type XIII, alpha 1 [Source:MGI Symbol;Acc:MGI:1277201]
Coordinates
chr10:61320336-61323232:-
Coord C1 exon
chr10:61323188-61323232
Coord A exon
chr10:61320378-61323187
Coord C2 exon
chr10:61320336-61320377
Length
2810 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
AACTTCCTTTTGGCTTCTAGGTT
3' ss Score
8.85
Exon sequences
Seq C1 exon
GGAGAGAAAGGAGAAGCTGGGGAGAAAGGCGACCCGGGAGCAGAG
Seq A exon
GTAAGTCAACCCAGCTCTTCTTTAATGTGATCATCTGACAAGGGCATCACTAGAAATACCAATTTTTCTCTGAGTCGCTTAGCATCTATGACTGGCGAAGGCCAGAAGCTGGGCAGCTGTTGGGTTCTGAGCCCCATATCCTGGGACTACAGTAGACATAGGAAAATAAATACAACTGCCTGGCCCAGGCCACAGAGGTCGAGCCGTTTGGGCAAGTTCTGAACAGATGCGTAGGACTTTGTCACGAAGTGTCGGAGGAATGCCTTCCAGAGAGGTAGGGTTCTTTGAGAGACATCATGGAAGGGGGAAGAAGATTGAGGAACAGGAAGTTGCTATGGACACGGTTGGCTGGCTGTGCAAAAGATGATAGCTCTGTGCATCAGGGGAAGCAACAGAGATCTTGGAGATGGGAGGGAGAAGATGTTTGGCAAGAAGGCCCGGGCAGTCCGGTAGCCACCCGAGAGCAAAGCAAGAGACCACCAAGAGTCATAGTCCCCCACAAGCTCTCCCGGCCCGTCACCCTTTAATGTCACCAGCCCCATCTGAATCAAGTGAAACGGACCTAATTGTTCGCTAACACTGTTCCTTATTAAGAATGGGATGCACCCTGAAGAGCTGATCCTAGATTCTGGAAAAGCATTATACACACAAATGTTCCTCCCAGGAACTATTTCAAGTCCAAATTGGAAACAGACAATATCCCTAGCAAGAAGGAAGGGATAAAAATCCTTAGGCTAATAAGCTAGTAGTAATAGCATTGCCCATGGCTGGGGGCCTTTCTCATGCCAAGAATGGCTTTCAGCCCTATCCAAGGAGATGGTCGCTCTCCTGCACAGCGGCCAGTGTTTCATCACAGAAGATGGCTCATAGGGGAACACAGCCAAAAATAGAAAAATCAGTTTTACATCAACTAGAAAAGACTAGAAAATCAAATTATATTTATGTATCCTTGTAAGTACATAAATGTCTCAGCAGTAGCTGAGATGTTTAAAAAGCTAGGAAGAAAACCAGGCAGAAAAATATGAGCAGTCTTCTCAGTTAAATAGGACAGAAATACATTGCTTTTCCTCCTTTTAATTCTCTTTCATTTATAAACTATTTAATAAGCCTGTGTTACTTCTAAACATTTTTAAGTTGCTATACAGGTAAAATGGACTATGGGAGAGTATATAGACGTTTAAAACACATAAAACAAGAATAGTTCTCATAAGCTGGACATGGTGGCACGTACCTTTAATCCCAGCACTCAAGAGGTAGAGGCTGGTGGATGTCTGCCAGTTTGAGGCCAGCCTGGTCTACAAAGCCAGTTCCAGGACAGGCAGGGCTGTTACACAGAGAAACCCTGTCTCAAAAAACAAACAAACAAAGAAACAAACAAAAGTACTTTGGTTGTTTTGGGTTTGTTTTGAGGCACAGTCTGACTATGTGGCTCAGGCTGGCCTTGAACTCACAGAGATCCGCATGGCTCCCGAGGGTATCACCACGCTCAGTGGAGTGTGGATTTCTATATGCACCCATACAATCAGATCTGTACATTATTTATTTATAATAAAAACTGTGCATGCATGCCTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCGCGCTCATGCGTGTTTTGCTGGAGGCAAAGTCTAGAGCCTTCATGCATGCTAGACCAGTTCTTTACCACAAAGCTACAGCCCCGTCCAAGTGCCCTAGTTACATTCCTGTTGCTGTGATAAAAAATACCCTGACTCCCCCCCCCCCCAAAAAAAAACCCAAAAAGCAAAAAACCAAACAAACAAAACAAAAAACCCAACCTTGGGGAAAACAAGGTTCTATTTAGCTCCCAATTCCAGGCTCTATGTCCATTGATGCAAAGAAGTCAGGGTGGTAGAAACCTGAATCAGCTGGTCATATCGCATCCATAGTCAAGAACAGAGAGCAATGAATGTGTGCATGCTCGCTCACTTACTCGGCTTCCTTTCTCCATCCATGCAGTTCAGGTACCCCTGCTTAGGGAATGGTGCTGCCCACAGTGGGCTAGCTCTTCCCCACATCAATTCACTATTAACCTACCACAGATGAGGCTGCAGGCCAACCCAAGGGAATAAATCCCTCACTGAGAACAAAGGCTGTGTTCTCTACAAGGAGATCCCATGGAGCAGAACCACCACAGTCTAAGGGACATTGGTGTTTTCTTATCCGGCTTAAATCCCTCTTGCTGCCCCTGCCCTCAAGGAAATACAACCATCACTAGACTATCCATTACATCTCAAAGGAAATACTGTCATGGGCCTGTCCATTACAAACCTGGGCAGAGCTAGTCTTAAAGAATATTCTACAGGGACATCTCAGCCTCCTCTGGCTTTAAATAACCGGTCTTGGCTCCCTTAAGCCAAGGATCTCAAAATCACATGTCTACCGGGTCCAGGTGACAGATGAGTGCCAAGAGGCCAGAGTTGAAGACAGCAGGGGGTGGAGTCTGGGCAGACTGGGGGTCATGCCTTACCTAATGGGCAAGACTCTTACTCCTTTCCTGGGCTGTGCTTGCCATACACTACAGCATGGCACAAATCCAGTGCTAGCTAAGTGCTGTCCCGGGTTAACCTGGAGGAGTAGGTGATCTGGAAACATTTTCTGAAAATGTGTTCGGGCCAGCACTGTGGAAGGCCAACAGTTTTCCCTGAGTTCCTGTCCTAAGTCCCCTTCAGGGTGTGTACTGGCCTGATCTTCGGTGTCAATCCTATCCTCCCATGACCTTAGCTGGACCGGGACCATAACAGAGCATAACACAACTTCCTTTTGGCTTCTAG
Seq C2 exon
GTTCCTGGGCCGCCAGGGCCAGAGGGTCCTCCAGGACCTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058806-Col13a1:NM_007731:32
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:
PF0139113=Collagen=FE(22.6=100),PF0139113=Collagen=PU(0.1=0.0)

							
A:
NA

							
C2:
PF0139113=Collagen=FE(16.9=100),PF0139113=Collagen=PU(18.3=92.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000090141f5093A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000042258, ENSMUSP00000090141, ENSMUSP00000101090, ENSMUSP00000101092, ENSMUSP00000101093, ENSMUSP00000101094
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr10:69932605-69935349 
ALTERNATIVE
HsaINT0038042
(COL13A1)
Human
(hg19)
chr10:71692361-71695105 
ALTERNATIVE
HsaINT0038042
(COL13A1)
Rat
(rn6)
chr20:31474666-31477360 
LOW PSI
RnoINT0038982
(Col13a1)
Cow
(bosTau6)
chr28:26378625-26382754 
LOW PSI
BtaINT0040914
(COL13A1)
Chicken
(galGal4)
chr6:10621854-10622626 
ALTERNATIVE
GgaINT0043075
(COL13A1)
Chicken
(galGal3)
chr6:12134783-12135555 
LOW PSI
GgaINT0043075
(COL13A1)
Zebrafish
(danRer10)
chr13:7735687-7737915 
LOW PSI
DreINT0007198
(COL13A1)
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"