Special

MmuINT0041396 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr6:121958324-121959459:+
Coord C1 exon
chr6:121958324-121958507
Coord A exon
chr6:121958508-121959299
Coord C2 exon
chr6:121959300-121959459
Length
792 bp
Sequences
Splice sites
5' ss Seq
ATTGTGAGT
5' ss Score
7.35
3' ss Seq
CTTGTTCCTGATGTTCTCAGATC
3' ss Score
8.73
Exon sequences
Seq C1 exon
GAAGTATATGGTGCTGGTCCCTTCTCAGCTCTACACTGAGACCCCTGAGAAAATCTGCCTCCATTTATACCATCTGAATGAGACAGTGACCGTTACAGCTTCCTTGGTATCTCAAACGGGAAGGAGAAACCTGTTCGATGAGCTTGTGGTTGACAAGGACTTGTTCCAATGTGTTTCCTTCATT
Seq A exon
GTGAGTACTATATACCTGTCCTGATTTATTTTATATTTATGAACATTTGTGAATATATATATGTAATATCCCTATATATTTCTTAAAAAGTTAATCTAGAAGCATATCAGTGAACTGAAAACAATAGAAATTTAGAACATTTACCCAATAAACAAATAGCATAGATCATCCCACCACAAAATAAGAAGAGACCATACTTGTGCATACACTGCTTTTCCATTGAATTACCTCAAAAAAAAAAAAAAGAAAGAAAGAAAAAGAAAAAGAAAAACAAAAGCCTATGGCCCAGAGAAAGAAGGGGTTTGCCAATTCATAATACTTACCACTAGTGAGTTAATAAACTTTCAAACAGCACTCCATCTAATTAGAACCACATTTCCTATTCATAATCCTGATATCCTGAGTAAAGCTGGGTTTCTTCTTTGGGACCTATCCTCAAGACATAATTCCTGTAACCAGTAATATATTGTCTTACTCTCAACCTCAGTTTCAGAGTTAGATCTAATTTTCTTTCATTTCTGAGAGTTAATTTTCTATTGAGATTCTATTTACTCCATAAAAATCACTGTGTTTTTGTGTCCGTATAAACTCACATTGACTTACACAAAATGTTGTGTTTTCATTTCATTACTTTTTCCATGACACTGTTTTTTCCTTCAAATAATCCTTAAAGAGAAACTGATGGACCCTCCACCTCTTTCCTGTGAGGTGGAAGGAGAGACTGTTAGTGAGGTATTCTAAGAAGTGATGAGAGTCAGATGGTGAAGGGTCTCTTGTTCCTGATGTTCTCAG
Seq C2 exon
ATCCCTACACTCAACTCTCCTGATGAGGAGGAGTTTCTCTACGTGGACATCAAAGGGCCAACCCACGAATTCAGCAAAAGGAATGCAGTGCTTGTGAAGAACAAAGAAAGTGTTGTCTTTGTCCAGACAGATAAGCCCGTGTACAAGCCAGGACAATCAG
VastDB Features
Vast-tools module Information
Secondary ID
-Cpamd8:NM_008646:2
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:
ENSMUSP00000080469





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Conservation


Human
(hg38)
chr12:9112537-9113359 
ALTERNATIVE
HsaINT0000035
(A2M)
Human
(hg19)
chr12:9355281-9356363 
HsaINT0135671
(PZP)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr5:101300894-101302075 
ALTERNATIVE
BtaINT0010518
(A2M)
Chicken
(galGal4)
chr1:75743340-75746950 
ALTERNATIVE
GgaINT0103735
([1])
Chicken
(galGal3)
chr1:79384536-79388091 
LOW PSI
GgaINT0103735
([2])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GAAGTATATGGTGCTGGTCCCT

				
R: 
TGATTGTCCTGGCTTGTACACG

				
Band lengths: 
343-1135

			

		

	





	
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"