Special

MmuINT0115081 @ mm9

Intron Retention

Gene
ENSMUSG00000021223 | Papln
Description
papilin, proteoglycan-like sulfated glycoprotein [Source:MGI Symbol;Acc:MGI:2386139]
Coordinates
chr12:85130105-85133332:+
Coord C1 exon
chr12:85130105-85130271
Coord A exon
chr12:85130272-85132781
Coord C2 exon
chr12:85132782-85133332
Length
2510 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
TTTCTCTCCTTGTCCTGCAGCGC
3' ss Score
11.43
Exon sequences
Seq C1 exon
GAATGGCCTGCCAATACAGGCCGACGGTCACCGTGTGCACCAGTCCCCAGATGGCACACTGTTGATCCACAACTTGCGGCCCAGGGACGAGGGCTCTTACACATGCAGTGCCTTCCGTGGGAGCCAGGCTGTGAGTCGCAGCACCGAGGTGAAGGTGGCCCTCCCAG
Seq A exon
GTGAGAAAGGCTCGTCATGGGCTTTGCTGTCCTGAAGGCAGCTGAGCACCAAGGGCCACGGGCACGTTCTCATCTGTGCTCACGTTCTGGTTACTGGCACTGTAACAGGGGTGGGTGTTTCTTATGGCCCCAGAGCCCTGCTTTACTGGGGCTAGCCCACCATCTAAGGCCATGGTGAAGATGTAGCAAAGTGGTCAGAGTTCTGTCATTCAGCTTTATCCCTAACATAATGTTCATGGTGGTTGGCTGCTAAAGTCCAAATTCTAATCAGGGTGGCAGAAGGCCCTGTGGGTCTGGGCTGTGGCTCAGTGCAGAGCTCTTGCCTAAGGCCTTAGGCTCTAGCCCAGCACCGTGACAAACACGGAGAACAAATAAATAGAAAAGGCAGAGGACAGATTCTTTGATCATTGTTGGCACAGTCTCCTTTCCAAATCACGTACAGTTTGTAATTTAAAGATAAAGATTAAAAATTTATATAAAAAATGGCTGTAGGATGGAAACGTGTGTTTTTGATCATCTAGGCATGTAATAGGATACAGTCACCCTCATCCTTTTTCCACGAGACAGGCAGCCAGAGAGCTGCAGGGTGTTCCCACTTGTTCACACAGCAGATTTGTGGCCAGCTGGGACTCAAGCCCAGGCTTTTTGACTCCTGATTTTACTTAACTTATGTAGCCCAGGCTGACCTTGAACTTGTTATGTAGCCAACGCTGGTCTCACCTTTAATCTCCCTGCCTCTGCTTCCAAGGTGCTACTGTGCCTGTTCTCTTAAGCTCCATCTCAGAACTCGTGAAGCAGGACTGTTTGATGTTCAAACTTGCAGGGGCTCTGTGTTTAAGTGACAGGGCAGGAGGGGCCCCTCACAGTGCTCTCCACAGGTCTTAGTGTTTCAGGGAGATGGAACATCAAACAGCTCAGAGCCTCCAGTCAAACAGCCAGTTCTCATAACCTGAGGTGCATCCCGAAGATGCCAGAGAAAGGGTTCTTGGCTTGGCGGTAATGGTACCAACTGCCTGGTGTGCTTGAACATTGCCGTGCCACCGGGGCAGGCCTGGCTGTCCTCCTGGATGCCAGACTGCGGGTGAGAACTGGCCAGGGGTTGAAGGTGTCTGCTACAGTGTTGCTTTGTGAGACTGACACTCAGGTTTCCCTCTGTGAGCTCCCTGGGACCCTAGGGCCCAGACAAGTGCTCTGCAATATGGAGACTCACACGGCTGTGACTGTGTGTGCCTGTGTGACCACACTCTGGTCAAAGTCCCATATGGCAGGACTTCTACCTTTGATGTTTCTAGAAAATCCTACTCATCTATACACTGATCAAACTAATAAGACCAGGAAAACCCAGAATGCAGATTTACTGTGGTGAAGAGAAGAGACCTTAGGAGACTGAGGATCTGAGCATGGTGATACATGGTGACACATGCCTATGAATTCTAGAACATTATCCTGACTTAAGACAAAACCTACCACACTACCAAACTCCTCAAGGGGACCTGGATGTTTACATTTGTGATCAGCCGTAGATGTGTCTACAGTGAGGGAAGCTTGTTTGACAATGGTGGCTAGTAGGCTTTTAGGCTTTTGGTGATGTGTGGCTGCCAAGCTGATCTCCCAGACACCACCCACGGCCACAGGCCTCTTTTGCTCTCTGCTGCATGTGGCTAAGAATATGTTCCATATTCTGGAGGCATCTCTCCAGAAGCCCGGCTGTCCCCCCCCAGCCTGTCTGTATTCCTTTCACTGACCAGGCTGCAGATCTGTTCTAACTCGTTGGTTTGGAGTCACATAGTGAGTGTCTCATGACTGGGAGCACTGGAGTTAGTTGGCTTAGGCTTTTCTCACCCTGGCTTGTTCTGCCCAAGGGTTAAGTGAATAGGATATATTGTGGGGACAAAGGCTGTCTGCTAACCATTCTGTCTGCCTCATTTTCTGAGGGGAGGACACGGCTGTGGGGCCAGGGCAGCAGACAGCACTCAGGTTTTTGCTGTGTGCCTGGTGGTAGGGACAGTGCTGCAAGAGCCTGCAGAGAGAAGGGGGGTAATTGTAGGATGAGAGAGTGGAATCAAATTCTTAACAATCACCAGACACTCGTAGGATATTGAGGGTGGCACGCGGGCTTGGGCCTCCGTGTAGTCTTAGAACTTTGAAGATTCATCACGTTCTCGGGTGGAAACCAGGAAAGATGGGGATATAGGAGACAGATGCAAGCTGGGAGGTTGGTGGAACCCAGTAGCAATAGGAAGATGGCAATGGCTTACTGACTTCCGGTTTCCCTAGGACTGACCCTACTGATCTTTCCTGCCAATCTGGGCCCATATAGCTGTCATTGGCTTTGCAGTTCCAGACAGTAGGGCAGGAAGTTAAATGTGGAGCCGTCGATGGTCTAGCCAGAAATAGGAAAGCCTGGAAAAGGCTGTGCACTGGGCATAGGCCGCAGATAAGGGTCACAGGAGGGCCTGTGAGAGGCTGCAGCGAGAGCTGCCTCAGCCCTTTCTCTCCTTGTCCTGCAG
Seq C2 exon
CGCCAGCCGCACAGTCCAGGGACCTAGGCAAGGACTGCATCGACCAGCCGGAGCTGGCCAACTGTGCGTTGATCCTGCAGGCCCAGCTCTGTGGCAATGAATATTACTCCAGCTTCTGCTGTGCCAGCTGCTCCCGCTTCCAGCCAAATGCCCAGCCTGTGTGGCAGCAGGGATGAAGGCTGGCTGTGGCGCCAGGTCTGGATAGTTTGCTGGGGAGAAGGGATGGTAAGACATGGCTTGCAGAGGGAGTCGTCTTTCAGATCCTGCCCCTCTCAGAAATCCAGGGTTGAGCCCCAGCAGCTGCCAGTGCCGGCTTCCCTTGTAGTGCTCAGCAGGGTCTGTCTGATATGACCACAGGCTGCTGTGAAGAAGAGGAACCCTTTACACCTCCCCTCTATAGTATCTACTGCACCGAGGACCTTTTATCTGAAATGCTTTGGACCAAAGTGTTTTAAGCTATTAAGTATTTGTAGACTTTACTAATTGAACGTCCCTAACCTAAAGTTCTGAAATGCTCCGAAGCTTCAAAGACCCAATCGCCATGTCAGCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021223-Papln:NM_130887:26
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.158 A=NA C2=0.034
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0767911=I-set=PD(59.8=91.2)

							
A:
NA

							
C2:
PF086866=PLAC=WD(100=59.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000113806





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000021646
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr14:73268724-73272494 
ALTERNATIVE
HsaINT0120122
(PAPLN)
Human
(hg19)
chr14:73735432-73739202 
ALTERNATIVE
HsaINT0120122
(PAPLN)
Rat
(rn6)
chr6:107273503-107276379 
ALTERNATIVE
RnoINT0107098
(Papln)
Cow
(bosTau6)
chr10:85121307-85123724 
ALTERNATIVE
BtaINT0107383
(PAPLN)
Chicken
(galGal4)
chr5:25589817-25590189 
ALTERNATIVE
GgaINT0053615
(PAPLN)
Chicken
(galGal3)
chr5:28476319-28476691 
LOW PSI
GgaINT0053615
(PAPLN)
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"