Special

MmuINT0023999 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr1:164608141-164609738:-
Coord C1 exon
chr1:164609631-164609738
Coord A exon
chr1:164608360-164609630
Coord C2 exon
chr1:164608141-164608359
Length
1271 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAC
5' ss Score
7.82
3' ss Seq
CTTTTTGTTTCTTTTTCTAGGTT
3' ss Score
12.86
Exon sequences
Seq C1 exon
GCAAGAGCAAATCTTACTCAAGCCTCAAATCTTTACTCTGGACAAGTACAGCAGCCTGGTCAGACAAATTTTTATAACACTGCCCAATCCCCCAGTGCTCTCCAGCAG
Seq A exon
GTAAACTATGGCATGGTAAATTTCCTCACTTTTCTATATTATTCTTTGTATTGATTGTTTTGTTGTTAATTTGACATTTATATAGAACCAAGATAGAGGAGGTGGTTTTCAGATGTACACCGGAATGTCGTGGGAATCCCATTAGGTCTATTGGAAGTGGAAGGCGCTTCCTTGACTCCTGTAACAGCTCCTCCTCCTCCTCACTGCATTCTAGGTTCACTTGGTTTATTTAAGCTGGGTTTATAAGAAAGGAATCCATGCATATGGAATTTTGAAAATCATTTATTAAAGAATATAGTACATTCAGTGTTATAGGTGAAAGAAGACTCTAAGATAGTGCTTTAATCCTGCACAAACATCATGACCAAGAAGCAAGTTGGGGAGGAAAGGGTTTATTCAGCTTACACTTCCATACTGCTGTTCATCACCAAAGGAAGTCAGGACAGGAACTCAGAAAGCAGGAGCTGATGCAGAAGCCATGGAGGGATGTTCTTTACTGGCTTAATATAATGTAGCAGAGTAGCACTAAGGGCAGCATCTTAAATGCCCTAGTATAATTGGACTTTTCAATGGGAAGTGACATTCTGGTAGAAGGCTAGAGGAGAAAAGCAAGCCATTAATCTTTTGCTTGCTTTTGTAAGGATGACAGTAATATCAACTTACTGTCAAGTAAGAGTTGTTTTATATAAACTGAAAAGACCTTTTACTTATAAACACTCAATTTGGTGAAACCTGTAAATAATATAGAAATATTGGTGAAAGGAACTTGAGCGATTTTAAGTGTATATTTTCTGGTATTTGATTTGTGCTCTGAGTATATTCAAAGTTAATACACGGTTTTTTTCACTATAGTTAACATATACAAAACTGTAAATCTTGACCTTGGTGTGATAATGAAAGCACCAAATCCCACATTTCTCCAGACTAGTAAGACAACAGATTGTCCCACCTCTCATACAAGAACAGGTATAGTTAGGGCTGATGGGCTGGGTGTGCTGCTTCATACCTTTAATCCCATCACTTGGAAGACAGAGGCACACGAATTTCTGTGAGTTCAAACCAGTCAGGACTACATAGTGAGACCCTGTCTTAAAGGGGAGAAAGCAGAGCTAGTTACTTAACCTAAAAGATTTGTATATACTATATATATTTGAAAGTATTTTACTTACATTTTTAATTTGATGATCTCTTGGTTGTTGGTATTTATTTAGACACAGGCACACAGTAATTACAAGCAAATGGTTACATTTTCTTTTTGTTTCTTTTTCTAG
Seq C2 exon
GTTACAGTACCTTTACCAGCATCCCAGCTTTCCTTGACGAATTTTGGATCTACAGGACAACCTCTGATTGCTTTACCTCAGACACTTCAGCCCCAGTTACAGCACACGACCCCACAAGCACAGGCTCAGAGTTTGAGCCGTCCTGCCCAAGTAAGCCAGCCTTTCCGAGGATTAATCCCTGCTGGAACACAGCATAGCATGATGGCGACCACAGGAAAA
VastDB Features
Vast-tools module Information
Secondary ID
-Bat2l2:NM_001081290:30
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
No protein impact description available





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
NA

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000028016





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028016f5784A, ENSMUSP00000038401, ENSMUSP00000038999
  



Associated events






Conservation


Human
(hg38)
chr1:171584527-171587002 
ALTERNATIVE
HsaINT0016721
(PRRC2C)
Human
(hg19)
chr1:171553666-171556141 
ALTERNATIVE
HsaINT0016721
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr16:39931298-39932610 
LOW PSI
BtaINT0118650
(PRRC2C)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr8:4842883-4844062 
GgaINT0035923
([1])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCAAGAGCAAATCTTACTCAAGCC

				
R: 
TTTCCTGTGGTCGCCATCATG

				
Band lengths: 
326-1597

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]










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