Special

MmuINT0039682 @ mm9

Intron Retention

Gene
ENSMUSG00000045672 | Col27a1
Description
collagen, type XXVII, alpha 1 [Source:MGI Symbol;Acc:MGI:2672118]
Coordinates
chr4:62934101-62937015:+
Coord C1 exon
chr4:62934101-62934145
Coord A exon
chr4:62934146-62936961
Coord C2 exon
chr4:62936962-62937015
Length
2816 bp
Sequences
Splice sites
5' ss Seq
AAGGTGATC
5' ss Score
4.41
3' ss Seq
CTTTGCTGGTGTGTACTCAGGGT
3' ss Score
8.07
Exon sequences
Seq C1 exon
GGACTGATGGGCGGCGTGGGGGAGCCCGGACTGAAAGGTGATAAG
Seq A exon
GTGATCGGAACTCTCCCTTACTGCCCGTGGGTTATCCGAGTGCCACTCCCCTGGGATCCCTCAGTGCTAGGCTCCTCTGCCTCCTACTGTGTCTTCCCTTCTCAGTCCTCTGCACCTACCATTCTGGCTTCTTTTGGTTTCTTGGTGTGTGAGGCTCATGGGGACGGCTGTGGAGGCCTGATGGTTAAGGTAGAAGACAAGAGAGGCAAGGGTCTACGGGAAGCCAAGGCTGACCTCTGAATCTCAAATGCAGAGCACGACAGCAGGAGTCACAGCCTCAGACTGTGGAGGGTGGAGATCTCAGAGGGCCAGCCCACACAGGTATCCCTAGAGAGTCCAGCACCCAGGCTGAAACTCTCTGGGAACCTAGGTCAGCATCCAAGCACCACTTTCCCCACTGGCCCTGGGAAGACCACTCCTAGGTCTAGCCACTGAACTTCCATTGTCTCAGCCCTGGGCCAAACCTTTTTGGAAAGGGGAGGTGAGTCCCAAGGCCCAGAGACAGATATTACCTATCCTGGATCACACAGCATCAGAATGACAGATTGATACCTGAGGAATATAGGAGTGCTCTGCCCTGTGCCGGCATCTCTTCCCTTCCCATCAGTTTCTATGTCAGTCTGAAATGCCAAAGAGTGTGGCATGTTTAGGGGCAGCACTCTGAGAATCCACAGGGAATGGCCTCCCTGCTCGGCGCCTCCTCACCTGGGCTCCTGCACCTGGGTCAGATGGCTGAGCCCTTGTGTCCTCTGGAGGCACGTGGGTCCTCGGAGAGTTCCACACCTGAACAGAATGGAAGTAGTAAGGTCAGAGTGGGTGAGTCTATTAGAGGTCACTTACTCTAGACCCTACTAGAGGTGACAACTGTGGAAACTGAGACTCAGAGAAGGGCAGATATTGATCAAATATCAATCAGATGATCATAGTTGATCCAAATCCCTGGGGTCTTAGGAAATGGAATTTCCCAGTGCCCATCCCACAAATAGGAGTCAGATGGTTTTTACTCAGTCCCCCTCAGGCAGCTGGTGAGATTGGGTGCTAACTTCAGCTCTTTATCTACCTGTTGCTACCTCTCTGTCTTCTCCCATCATGCATAAGCCTATGTTGTGGCCCGTCTAAGCTGGTGCCTGGTATGGCCTTTCCACCCCTCTTTCTTCTCTGGACGTGAAAGGCTTGTGGGGGTGATGGGGCTTCCTGACACCTGTCTGCTCTAAGACCTGAGACAGCAGCTCTGTGGAATAGCTGAAGGCCTGACCAAGGAGAGAGGGCATGAGTAGATAATGTCACAGCAGAGGACTTTGCAGGGCTGTCTGCCAGTGTGCTGAGCTAGGATGCATGGAAATGACCGTAGTGCTATCACATCCCTGTCACAGTGACTGGCACCACCAGGGGCACTTCCAGTGTTTAGCTCTGGAACACACTGAAGGAAGAGGAAGTCATTGGAGGCTGTTTTGGATGGTAGAGAGGGGAGAAGCTGTCCTGCCCTTTGGCTAAGTCAGGGTCTCTGGCTTGGGCTCTGGAGGCCACATACAAGCTGCCTCTACCTCCCAGGACCACAGAGCTGCCGTTCATCCCTGTATTCTTCTTCTCATTTTGACTTTCCATGACCCCACCTGGCCCTAAGCCAGGCAAGGCATATCCTGGAGTGAACTCCTGCTCAGCCTGTCTGTCTGGATCATGTCTTGGTTTTCTCAGTGACTTTTTTTTTTTCAAGACAGGGTTTTTCTGTGTAGCCCTGGCTGCCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCAAACTCAGAGATCCTCCTGCCTCTGCCTCCCAAGTGCTGGGATTAGAGGTGTGCACCACAACTGCCCAGCTCTCAGTGACTTTTAAACTTTCCTTCTCCATATTTTAATATTTGTTGCCCTTCTTTTCACATCAGAGAGAGAGAGAGAGAGAGAGAAATATGAATACCTCCCCAAACTCTATGACCTTGTACAAGATTTTCCAAATAGAAAAAAAAAGAAAAACAAAACAATTTAAAAAGAAACTTTTCAATTCCAATTTTGTTCTGATGATGGAGTTGTGTGCCATGTCACGTTTGCTGTCACCTTGGCCTTCTGAGATTTCAACTTCCTCCTGCTGCTGGGGCTTCCTGGGGCCTCAGTGAGCAGGCCTAATAGGCTACTGGGAAGAGCTCTCAGATGGCTCCAGTCCTAAAGCGAGGCGCCTTTCCATCTGGCCTGAGAACAGTTTACTTACCAGAACTGGACCAGGAGGGAGCCGAGGAGGTCTCCCACTGCCAGTCCTGTCACCAAACATTCCCAATCCATCTTAGAAGGGACCCACCCAGAGTTCAGTCAGGGCCCGTTTGATTCTCATTGCACACAGTCTTAAGAAGCCAGCTCTCTGATGCCTCCCACGATCGCTGATTAAGCATTTAATTAGAAGCCGGCTGCTTGTACAGAAGGAAGACATGACAACTCACAGCAGGCAGTGCCTGGGCTGTCATCCCTGTAGCTTTCACCCTTTCGTGCTGACATCAACTGCTGCTCAGGAGGCAGAAGGATGAAGAAATTTGTCCTATGAGAAAGCCAGTGTTCTCCATGAAAGGGCCAGGGGGCCTTGCAGTGCTCTGAGCAGCTGTGAAATGGGAGGGATCACCTCACTCTGGGCCTCCTTACCCTACCTAAGGGGTGGGTCCTTGATCCCTTTAGAGCCAAGGCTGCTGCTGGCCACAAGAGCAGCCTCCATGAGGCTCCATGGGGTCCTCTGTTCGGGGGTGAGGGGGGAAGCTTGCAAGTTGCTGGCTCTCTCCTTATGATCTCTTTGCTGGTGTGTACTCAG
Seq C2 exon
GGTGAACAAGGGGTGCCAGGTGTGTCGGGAGATCCTGGCTTCCAAGGAGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000045672-Col27a1:NM_025685:16
Average complexity
IR-C
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:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000043816





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000043816f4553A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:114231867-114235598 
ALTERNATIVE
HsaINT0038724
(COL27A1)
Human
(hg19)
chr9:116994147-116997878 
ALTERNATIVE
HsaINT0038724
(COL27A1)
Rat
(rn6)
chr5:79111703-79114480 
LOW PSI
RnoINT0039514
(Col27a1)
Cow
(bosTau6)
chr8:105229395-105232681 
Chicken
(galGal4)
chr17:4718615-4724332 
LOW PSI
GgaINT0125567
([1])
Chicken
(galGal3)
chr17:5356346-5362063 
LOW PSI
GgaINT0125567
(COL27A1)
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"