Special

MmuINT0039642 @ mm9

Intron Retention

Gene
ENSMUSG00000058897 | Col25a1
Description
collagen, type XXV, alpha 1 [Source:MGI Symbol;Acc:MGI:1924268]
Coordinates
chr3:130249278-130252161:+
Coord C1 exon
chr3:130249278-130249340
Coord A exon
chr3:130249341-130252092
Coord C2 exon
chr3:130252093-130252161
Length
2752 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TATCTTGCGATTTGTGACAGGGT
3' ss Score
5.44
Exon sequences
Seq C1 exon
GGAGAACCAGGCTTCATTGGTCCTCAAGGAGAACCAGGGTTACCAGGGCTACCAGGAACAAAA
Seq A exon
GTAAGTCGACAGTTATTCCCTTTACTTTCCTGTGAAAATTGGGTCATCTCTGTCAAAAGAAAGGTGAGATGACTTTGCTATTTAGGTGACCAGATATTTCTGCCTTCGAACCGAGGCAGCGTGATCCACCCAGGCATGCAATTGGAAGTTATATCCAGGAAGCTTTAGGAACCACTATGGGTGGATGGAATATAGTAGTTGTTAAAGATTACCCTCTAGATTCCTCAGTAAGTGTTGTGATGCTGCTGGCTTCCCAGCTACCTGGAAAGGTAGGTAACTAAGCAGAAAGGAGGGCTAGAGGTGGCCATACCCTACTCTTCCTCATCCATCTTTCGATACATTTGTAAACTGGACTCTAATCCCATCCCCACGGATGTTACAGAGATGTCTAAACGCTTCATTCCACAAGGATCTACCCTGAGTGGTATTTTCAGAAGTATTCTATAATGAAAACCATCTCTTAGTGTTCTCTTTGGCAACCATAAAGAGGACCCTGAAAGCAAAAGCTGTATGCTGCTGCCATGCAAAAAGAATGCAGTGCTGCAGATAGTGTCAGGCCTGGACTTCTTGCTCTATTTACCCAGAAGACCTAAAAAGATAGGACTCAGATGATGGAGCTGTGCTCATGACAGACTCATGAATCAAAGGGACAAAGTGGCATCAACATGTAGTCATTTATTTTTGAACCACGGCAGAGTCTGCCTCGGTGAGTTCTGCATTCACCAGAAATAAACCAGGGATGATGTCCAATAGTTAAGGAACTGTGTCATGGTCTATTCAGACAGACTAGTCCTCATGTCTGCTTTGGTCAAGTGAAAATAACTCTAATCCTAGGGAGTAGAAACTGTTCATTGCCTAAGGGGACTGGAACTCAGTAGGATTATGCAATGGTTGTTTTCCAAAGAAATCTCACTTTCACATAATGAGCTATCAGGCCCATTAGCAAAATATGGAAATTTTCTGTTTAAGCCTGAACAGATTCACACAAGACAGACCTTAGAGAGGAAATAAATTGTCTATTGATATGAAAATGGTTGGATTTTTTTGGAGCTTGGAGCTTTAAAGCCAGGAGAGGAGAGAAGGTGGCCAGGCAGAGAAGTATACCCACCACCACAGGAGGAGCGGAAGTTCCAGCAGGGGAAGCCATCGTGATCTCTTGCAGATTTTTGCTATACAGAGGAAGGTAGAAGAAACCCAGCTGGTGGAGATACTTACCCCTAAATGCCCTTTCGATAGATAGCAGCTATACCATTCCATAGCTCTCTTGAGAGGGATATCCAGTCATAGAGCCATGAAGTTGGCAGTAATTGCTGTTATAAAGGAACCCAGCATGATTCTGAAGAGCAGATACTTTACTCTGAAGCTCAAAGAGAAGGAAAGGATGTGATATACCTGTGTGGTATTTCTACAAGCCAGTATATGCATAGAAAGCCATTTTCAGCAATATTCTAAACGTGATTGTTAGCTGAATTGCCTGTCTTAACAAGAGTTGGATCCTAAAGGAAAATCTGCAATTTGAACATCTATTGCGACCCAACGATGGTCTTTTACAATTTTTGTACTGGTCTGGATTTGTACCCCTAACAATAGATCTAAAAAATAAACAAAGATTGTATCTCTAACTTGCTGGGCAGTGAAGACAGATTCTAAGGAAGAAAAACTAATAGCATCTAGATATCTGTAGTAGGGATGGCGTGTCACCTAGGACTGTCCCTGTGCCTTTGTCTAAGCTACATCTGCCTAGAAAACTTAACTTTCTGTCAGAGTATAAGAAAACAAGGTATCACAGTACAAAGCATGGAACTTCACCACTGTGCTAAACGTTCTGCTAGAATTACTTAAAAATTGCTACAGAATGTAAAATTGTCCACTTTATAATAATAATAATATAATAAATTAATAATAGACCATACTGATACCCTTTAAAAGTCATTACATTTACTCATATAGCTGTATTTAATAAACTATTATTTCCTTGTTTAAAGAATGGAGATTATAAGGAAGGCTTGCATTATTACTTGAGTTCTAGAGACACAGAAGGAACATCAATGAGTGAATGGGTGGGTGGATCAGTTGCTAGGTAGGTAAACACGTATGTACTTACATGTATATATACATATATAAACATAGACATGGTTAATGAGGAGATTTATTAGGGGAATTGACTCTTGTGGCTATAGAGGCAAAAATGTCCCACATAAGCTATCCTCAAACTAGAAGGATGCTAGGAATGTGGTTCTACCCTGGCCTGAAGGTTTCAGAATCCTGGAAGCTGATATTGAAACTCTGAAGCAGCAGTAAAGGTCTGGGATGCAGTGCCTGGTGCTAATCTTGCCATTGGGGCAGAAGACTGCAGTGTGGTATCATGGGCAAGAAAGGGAGCTACAGAGGGAGAGACGGCTTGGCTGTCTTCTGCCTTTTATTCTATCCATCCAGAGCCAACTATTTTAAGGGTAAGCCTCTCCCACTCACTCCACTAACCGATGTGCAGTCTCCTCCTAGAAACAATAAGAATGTTTCAGCAGTTCCATAGGCGCTCGCTGGCCCAGTCAAGATGGCACCAAAAATGAACAATCTCAGGTCGGTTTGTGCACATAGCGGGATCAGTCATCTTCAGAGATTAACATAGCACCAGTGCACTGTGGATAAGCAGCGGCTCTCTGTTAACCTTGGTTTTAGTGAACTCCTGTATTCTTTGCCAGAGAACAGCCATGGGGTGGCTGCTATTTATCTATCTTGCGATTTGTGACAG
Seq C2 exon
GGTGATCGTGGGGAGGCGGGGCCTCCTGGAAGAGGTGAACGAGGAGATCCTGGAGCCCCGGGGCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058897-Col25a1:NM_029838:19
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=PD(18.8=52.2),PF0139113=Collagen=PU(26.7=69.6)

							
A:
NA

							
C2:
PF0139113=Collagen=PD(18.8=52.2),PF0139113=Collagen=PU(26.7=69.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000079210f5095A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000076688, ENSMUSP00000079210, ENSMUSP00000079210f5096A, ENSMUSP00000101954, ENSMUSP00000101960
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr4:108863388-108869087 
ALTERNATIVE
HsaINT0038693
(COL25A1)
Human
(hg19)
chr4:109784544-109790243 
LOW PSI
HsaINT0038693
(COL25A1)
Rat
(rn6)
chr2:235660955-235663651 
LOW PSI
RnoINT0039468
(Col25a1)
Cow
(bosTau6)
chr6:17619485-17623702 
LOW PSI
BtaINT0041425
(COL25A1)
Chicken
(galGal4)
chr4:37060847-37061675 
LOW PSI
GgaINT0070689
(COL25A1)
Chicken
(galGal3)
chr4:38911035-38911872 
LOW PSI
GgaINT0070689
(COL25A1)
Zebrafish
(danRer10)
No conservation detected
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"