Special

MmuINT0039541 @ mm9

Intron Retention

Gene
ENSMUSG00000079022 | Col22a1
Description
collagen, type XXII, alpha 1 [Source:MGI Symbol;Acc:MGI:1916950]
Coordinates
chr15:71628906-71632384:-
Coord C1 exon
chr15:71632307-71632384
Coord A exon
chr15:71629951-71632306
Coord C2 exon
chr15:71628906-71629950
Length
2356 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
TCTTTTGCTTCCTGGGCCAGGCC
3' ss Score
7.23
Exon sequences
Seq C1 exon
GTGAAAGAGGAGCCAAAGGTGACCCTGGCACACCTGGAGTTGGTCTCCGAGGAGAGATGGGTCCTCCTGGAATACCAG
Seq A exon
GTATGAAGGATCAGGGTCTCAGCCTGGGTGAACATCAACCATGGAGGCAGGGGCACACAGTGGTACCCTCGCTTGTGGGAAGAGAGGAGGACCTGGGCCACTCTAAGGAGAAAAAGAGAACTAGTTGTTTAATGGAATATTTCTCAAGTCCCATGAGGCATACCTTCTAAGTTGAAAGTCCCAATGACTTATTTACTATTCCAAAATGACCAGAATAAAGTACATTGATGATATAAAGGTATGATAAATATTTGGGACGATTCAGAAGCAAGTTTCTCCAATTTGTTCATTGCATATTGTACTCATATCCCCCTTAAAAAATCTCATTGTAGGGCGGAATATTTGGCTCAGAGATTAGGAGCACTATCCGCCTTTTGTAGAGCAACTGGTTTAATTCCCTGGCAGGTCACAAACTTCAGGGATTTAATATCTTTTTCTGGTATCCACCAATACTGCAAGTACATGGTGCATGTACATAAATGAAAGCAAAAGAGAATATACATGAAACATAACTAAATAAGTACTCATTAAATACACATCATGCCCCAGAAATATACAGAATTATTATGTTCCAATTAAAACTAATAAATGACTAAATATTGTGAGAAATCATCATGGGGAAAGAGAGATTGTTGTATTCTAAATGAGTCTGGGCATGTTGGAGATGCACCTCTCCTTAGGACTTTCCTTCTATACTTTAATTCATGGTAATTGGTTAGAACCCCACAGGCAGAGCGACAGCCATCTTCTTAAATCCCATACTAATTCATTAGTATTTCTCAGAATAGGCCCAGGGAGCCTTAGCCAAAGGTTTAGCTAAAGGCCAGCCCTCCTGGAGCTGAGAGGTGGCAGGGTCTTGGGACTTTTACTTCTGAAACTTAGAAATAACTAGGGAAATGGTAGCCAGTTGACCACTGTGCCTTGTGGCTGTACTGAAAGAGGTCCTGAGGGTAGCAGCTGTCACACTGGAAAGGGGAGAGTTACAAGACTCTCAGCTCTAGATTGTCAAATTTTACCTCACCATCGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGTGTGTGTGTTTAAGTATGTGTATGTATTTGGGGAGCAGTGCTAGAAATTGAACTTAGGGCCACATGCATACTCTACCCTCAATCCTGAGGATTTTACCTTTTAATTTTAACTCCTAAATTTTATGCTTACTTTGTATCATTTATGAAATCTGACCTATATGTAATTTAACTTTAGTTTTTTCCTGCCAGGATTTCTCAAATTTGCTACAGTTAGATATGTTTTCTATTAGAGGTGATGATGTTACATGAATATTGTTTATATCTTGCTGATTTTCAAATATAATATAATATAAATACTACTCTGAAATAGGAGAAGTTATAGAATGGCAGAGTGTAGTCCATCTAGAACAGAGTGTGTGCGTAGACTATCTGGCAGATTACACCTGGCAAGGTTGAATCAGAGACCAATGGCAGTACATCTCAGTGGAAGAGATGCTTAACATAGATGAACCAAGAGTTTCCTTTAAGCAGGGCTGTGCACTAAGTAACCCTTGTCAGAATATCAGCAGAGTTCCAAAGTTCTGAAGATACTCACAGTGGAAAGGTTCACTTTTTGTTTTCGTTCTAAGAAATATTTTGACATCATGCTAAGATGTGAGGGAGAGTTTGACTTTGGAGAGCATGGTAGCCAAGTTGGCTACCACACCTAGTACAACGCTTCCCAGTTGTTCAGGCAAAAGAAGAAGCTAGATGAGTTACACATGATACTTGGTAATTGTAGGCAAAGCAGTTTATTTATATGTAATATTCTCTCAGTCTAAATTATAGACTCTACAATGGCCAGTTATGTATATCCTTGATGCTATACTTTTTACTTGGTGTAATAGAATAATATAGGTAAGTATGTGGTTCAGATTTAACAAGTTGAGGAAAGATAATAGATCCCAGACTATTTGAATGTTGAATTTTGCAGGATCATCAGATGTCCCTGTAAGAACAGGTACACCAGTCTATTAGACTGTGTGTGAGAATAGCGTTTGGCTTTCTCATCTGACTTGAGTGGAAAACTTGCACTCCTGGGGCCTTGAGTTGCCCTTGTCTGTTTCTCCTCCCTGGTGTCTGGATTTCTTCCCTATTTCAGACAGTGAAGGTTCTGCTCCTGCTTTCAAAGGTGATGTTCTACCTGATGCCCACACGGGACTTTCTCTTTCTCAGTCTAGAGCACCAACAGAGACTATTCTCTCTGAGAACACATTGAACCATAGTTCACAGCACAGATTACAGGGCTGTTTCTCTCCTGGATATAAAATGTAAACTGCCTTCTGTTTCTTTTGCTTCCTGGGCCAG
Seq C2 exon
GCCAACCTGGGGAACCTGGATACGCTAAAGATGGACTTCCAGGAAGCCCTGGTCCTCAAGGAGAGACAGGACTAGCTGGACATCCTGGCCCTCCTGGTCCTCCTGGCCCACCTGGCCTGTGTGACCCCTCCCAGTGTGCGTACTTTGCCAGCCTTGCTGCCCGGCCAAGTAATGTGAAGGGCCCATAGAAGATTCTAGATCATCAAAACACTACTATGGATTTCTGAAACTTGAACTCGGAGCCCATTGGGAAGCCAGAAGCCTTGAAACATTTCAAATCCTTCTTCTCTCTCCCCTTCCTACTTCCCGCCTTTTCTTCCTGCTTCCCCTCTTTCTAGTCTTTTCTCCTTGCCTGCCTTAATTGTCTTTTCCCGTCCTCAGAGACCTCACAGTTATTAAAACCAACAGATACTGTCAGACAGTCAGGTTATTATTAATATTATTGTTATTGTTTGCTGTTATTTCAAAGGCTAATAGTTTTGAGGGAGCTTCCTGGTGGACAGGAAGCAGTTTCCTGGCTCAGCTCCCCTGTCATCACTGGCTGAAGTGTGACAGCCAATTTCTGAGGAACCCTCGGTGCTATGCAACCCTGACCATGTATGCACTTGTTGATTTTACCTCTTTCCTGGAAAGGAAGCTTTAAGGGATGGAGACTGTATTGTTGTTTCCTCAGCTGTGCCTAAAGATGGCCCAGGGAAAAGTAAGTTTGAAATCCCCACCTCTCCAGAGAGACTTGAAGCAAGAAGAAGAATTTGCAGCCTAAAAGAATTCATTGACCTCTGGAGACAAGGTGCACATCTGGAGTTCAGAACTGCCTCAGGGCATTGGGGGGAAGGTGGTTATCCTTGGTGCTTCAGGCTACCAGAACTCCAAAAGAAGTCACATAGTATTGGCAGTAGCTTGTGTCAGGGCCCTCTATGAACAAGCTGGTGCTGAAGAAGAGTTCCCAGGTGTGACTTCACTTCTAACTGTGGCCTGAACCCCTTCAAGTTCCTCATGCTGGTTTCAATTGTGTGAGTTGCAAAATAAAAGTTTTCAATGGTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079022-Col22a1:NM_027174:63
Average complexity
IR-S
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(23.3=51.9),PF0139113=Collagen=PU(24.1=51.9)

							
A:
NA

							
C2:
PF0139113=Collagen=PD(74.1=68.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000125069





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr8:138589441-138591423 
LOW PSI
HsaINT0038592
(COL22A1)
Human
(hg19)
chr8:139601684-139603666 
LOW PSI
HsaINT0038592
(COL22A1)
Rat
(rn6)
chr7:113015935-113018400 
ALTERNATIVE
RnoINT0039405
(Col22a1)
Cow
(bosTau6)
chr14:5353310-5353569 
LOW PSI
BtaINT0041395
(COL22A1)
Chicken
(galGal4)
chr2:144145919-144146894 
LOW PSI
GgaINT0090628
(COL22A1)
Chicken
(galGal3)
chr2:150186903-150187878 
LOW PSI
GgaINT0090628
(COL22A1)
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"