Special

MmuINT0036103 @ mm9

Intron Retention

Gene
ENSMUSG00000056486 | Chn1
Description
chimerin (chimaerin) 1 [Source:MGI Symbol;Acc:MGI:1915674]
Coordinates
chr2:73544976-73548543:-
Coord C1 exon
chr2:73548512-73548543
Coord A exon
chr2:73545090-73548511
Coord C2 exon
chr2:73544976-73545089
Length
3422 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
GAACTGGCTTTGTTCTGTAGGTA
3' ss Score
7.84
Exon sequences
Seq C1 exon
GTAGAAAACAGACCAAAGTATTATGGAAGAGA
Seq A exon
GTAAGTATGGATTATCAGAAAGTATCTCATAGATTGTCATATGTAAAAGATACAAATAAATGCATGGTTTTGGTAAAAACACAGGATGAGATAAATATTCTAGTTTGGTGGAATTGAATTCTCTTTCTTTGATTACAGGTGTAATCCTGACTAGTCTAAATAGGAAAATACAGACAAGTATAAAAAGAAAGTACCTTGATAAACAAATGTGCAATAATGCTAAAGAAGCAAGCCATATAGATACATACTCCTAGATGGATCTCAAGAAAGTGTTTATAGTTATGTACTAAATGCAATAAAACATATCTATAGACTCAGTGGGTATGGACACTTTATTTTATATTGCCCCCCTTTCTAGTTTTCTATATTGTGTAGTATCAGCCCAGAAAAGAAGTGATTTGTGTTATTCAGAGACATGTCAAAATTTTTATATACTACCTTCTGAAGATGTTTTCCTAATGTTATTTTATTTTTTAATGTACATTGGTGTTTTGCCTGCATGTATATCTGTGTGAGGGTGTCAGATCACCTGGAAGTGGAATTATAAGCTGTCATATTGGTGTTTGGAATTGAACCCAGGTCCTCTGAAAGAGCAGCTCTTAACCACTAAGCCATCTCTCTAGCACCCTTCCTAACATAATTATTTAAAGCAGTGGATCACTATGAAGGCCAGCTTCCTTTTGTGTAAAATTATAGGCATGTGCCAATGCATCAGTCCCCTCTCAGGCTTTACAAACATCTTGTCCATACAAACTTGTAGTTTGAGTTTTCCACTTAATGTTGATAATGAGCATTATAATATTTTTTTTTAAATTGCCTTTTGGTTTTAGTTCTACAGTTGGGCAACAAACTATACCAAAAATTATTCCAAATGTTGTTTTAGTGTTTAAGGTCTTAACTTTTCTGATTATTGAGAATAGAAATATAGCACTTTGAAGAAAAGAATAAAAATCTATATAAAAGAATATAGTCCATCTCACTCCCCAGATAAAAACTTTTGTTTTTCATTGGGATAATATCAGATAACAATGTATATAGCAAATATTTCTAAATTACTTAAAATTCCAGCCATGGGCCAGGTGGTGGTGGCACACACCTTTAATTTCAGCACTCAGGAGGCAGAGGCAGGAGGGTCCCTGTGATTTCAAGGCTATCCTGATTTACAGAACAAATTCCAGGACAGCCAGAAGACATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGACAGACAGACAGACAGACAGACAGACAGACAAACAGGACAGCCAGAAGACCTAGATAGATAGATAGATAGATAGATAGACAGACAGACAGACAGACAGACAGACATACAGACAGATGAACGACTGACTAACAGATGGACAGACAGACAGACACACAGTGTGTGTGTGTGTGTGTGTTTTTTAGTCGTGTGAATGTCCGTAGGCAGTGTACCTGTGGGTTGAGGTAAGAAGACTGCATAGCTGAGGACCAGTGACCTTAAGGGTTCTTCAGTTGACCTTCTGATTGAGGCTCTCAGCAGGAATGCTGGCCACAGAAGTGTATCTGATTTTAGACTGGAGATTTATAGATTAGGAGGCTTAATCTCTAACGCTAATAGTTATTTTGAGAAGCCTCTTATTGTACAATTTTAAAGGGATACAATTATTGGATCAATTGGTATGAATCATTTTAAGGGTCTTTAAATTTCATTGTCAGAGTGTCTTTCAAAATTTGAGTTTTATTGCTTTAAGATGATTGGTCTTTATTTTAAACAGCTAGCACATTTTGCCAAGTTTATTCACTGATGGCACATATAGTAATCTAATGAGGGTGTCACATCAAGGGTGGGTTACAATTTTGCTTGCACCAGATTCAGTGTATTGCCCGTGGACCTCGTTCTAAACAATTAAGAAATTCATAGAAATGAAAAATTCAGGAGACCAACTAGAGCATTTCTGATTGATGTGATTTAAACATTATTGCCATGCACAATTTTAAGACTGTTCAGAGACTGGGCCATACCTACAAGGAAAAACTTCAGAGAGTTACCAGTTATTCCAAGCAAAATTCCTGGGTTATTAAGGTACCAATAAAGGGCCTTTAAAATGTATTACAAAGTCAAGTGACTATTGTCCTTTTGCACTGTGGGAGCCACAAGCAGTGCTTCTTTTAAGTAGTGAGGCAGCAGTGATGAGAGAGACTATCTCCATGCTCTTCTGTGATCTCTGAGCCTTTGAGATAAATTGAACAGACAGATCACAGCATGGTTGATGTAGTGCAAACAAGGGCATCACAGGAGAAGTAGTATCTACCCAGTGAATTGTCTGAGTTTGTATATTAATATTTTATTATTTATTTACTTTTTAGTAATTTAAAATGCCCTTAGGAACATTGTGGGACAGTTAGGGGAGAAGTGATTTTTAGGAAATATGATTTGTCCCTTAGGAGAGTGAATGGGAGATAAGCTAGTTTGTAGTAAGATTTGTGTGGTGTGATATCACCTTAAATCTCCTCTTTAGGGGAAACTCTGTCTCCCTGGGAAGGAGTTTGCTGGGACTTTGCTCCTTTTGGATGGTTTGTCTTTATGTAGAGAAGGAAGCTCAGAGAAAGATGTGCTGTCAGGTGAGATAACACACTGAAGCAGCACATTCCACATGGCAGGGCCCATAGTCCTTGGCGGTCTTTGAGTTCCTAAAAGGATTTAGTGTGTGAGTTTACAAATTGCAAATCATCATACAGGTCTGAATGATTCCATGTTTTAGATATTTGCCACCACTGCTATTTTTATTTTCTTAGTGTTTTATATCAGGGTGTTGTAAATGAATCTTTGCATAAAGGATTTATCTATTATTTGTGTTTATTCTTCCTTCTTTCCTTTGTTAATGAAAGATAGATTTGGGCAGGAAGTGAAGGCAAGTGCTGCCCCGTTTGCTTGTGGTCTGAATATTGAATGATGCGCATCATGCACATCACTGGCTGACCATGATAATCTAAAGACCCAGGGCCCTGGGAAGTTGCCAGCATGGACTTCCAGCTAGAAGTTTGGACCACAGCACCAACTGCGAAGAAGAAATGAGATACATTTCTGTATAGTATTCTTTAGCAAGCCTATATGGTCACATGGCCACATGAGAAAGGCCACATGGGTAAGGTGGAGGGTTCTGCCTCAGATGGATGTGGATTTTGCTTCTGGGCTGGGAACTAGACTCAGTAGCCATTTTGGTGCTTTTCTTATCATAGAGAAGCTAGCCAGGAGCCAAGCCAGAGACACACGCACAGTTAAATCTGAGTGCTTTTCCTTGCACTGTAGCTGAGAACAGCAGGTGAGGGCAGGGGTTCCTTGTCCTGTTATATTAAAAAACATGAGAAGCTGTGTTTCTGAACTGGCTTTGTTCTGTAG
Seq C2 exon
GTATCATGGCATGATCTCTAGAGAAGAGACTGACCAGCTCCTGAGTGTGGCTGAGGGGAGCTACCTCATCCGTGAGAGCCAGCGGCAGCCAGGAACGTACACTTTGGCTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000056486-Chn1:NM_001113246:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.057 A=NA C2=0.060
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0001719=SH2=PU(0.1=0.0)

							
A:
NA

							
C2:
PF0001719=SH2=PU(53.5=97.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000107655





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000107655f5005A, ENSMUSP00000107655f5006A, ENSMUSP00000115029, ENSMUSP00000116708, ENSMUSP00000123312, ENSMUSP00000128847
  



Associated events






Conservation


Human
(hg38)
chr2:174915172-174918533 
LOW PSI
HsaINT0035038
(CHN1)
Human
(hg19)
chr2:175779900-175783261 
LOW PSI
HsaINT0035038
(CHN1)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr2:21951853-21954220 
ALTERNATIVE
BtaINT0038232
(CHN1)
Chicken
(galGal4)
chr7:16243296-16244399 
ALTERNATIVE
GgaINT0047729
(CHN1)
Chicken
(galGal3)
chr7:17897773-17898877 
LOW PSI
GgaINT0047729
(CHN1)
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"