Special

MmuINT0132605 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr17:3193014-3195993:+
Coord C1 exon
chr17:3193014-3193082
Coord A exon
chr17:3193083-3195777
Coord C2 exon
chr17:3195778-3195993
Length
2695 bp
Sequences
Splice sites
5' ss Seq
CATGTGAGT
5' ss Score
7.83
3' ss Seq
TTTTTGTCTGATTTAAACAGCTT
3' ss Score
7.23
Exon sequences
Seq C1 exon
GTTTTATGCCACCTCCAGTTCCCCCACCTGTGGTACCTCCCCCTGCAATCCCACCGGTAGTACCAACAT
Seq A exon
GTGAGTTTTTGATTTACAAAGTGATTTACAAAGTCTGTTTTATTCTAGGGAGTCTTGTATGTTTGTGCTCATTCCTATAAAATACTGGTTTTTCAACGAACATGTGTTCAATGATTCTGAACATTGACAGCATCTCACAGTTCTTACTCATATATAGTCTCAGTTGTCATTGCATAACCTGCTCCCCTTAGTCAAGAGAAGCCATCCATTGTCATTGTGATTTTGCTTGGTTGCGTTTACTGTAAATGTCTTCCTCTAGAGCCCTGCTGCTCAGCTGCTTTCTAGATACAAGACTGCTGTAAGGTGGAAGTTAGTGCCAAGGACTTGTTTGTTTATATCATGGATCACCTTTTCCCCACAAGGACACAGCAACATGTCCTAGACTCGTACCATATCTCACTAGTGTCTTTCTGTTCATTTTGAATAAACAGATACTTTTTAACAAAACCAAGCAGAAAGTACAGAAATTATTTGTGTGCCTCTGTCCTGGCTTGTGCCAGAACATCATCTCCACTTATTACCATCCCCACTAGAGTGGACCTAGGCAGAGTAGATTGACTATCTATATACCTTAGGTATAATTCTGATACATAATTTATACTATGGTTTGCTAACTTATTTAACAGTGTTAAGATTGAGGATATCCAGGTATTGCAATGAAACCATTGAAATAAATGTTTGCCTGTTAAGTTTTTAATTGTTTGTATTTGTTGATTATTGTTAGTTAAATCCATTTATCATTATTAATTGCAAATTAGTTATCTTTCTAAGTAGTACTTCCTTCTGCATTCCTTTCTTAAGGTTTTAATGTAGATGTAGTGAAAACTTGCCAGGTGATGGTGATTAGTCATCTTGCAGTGTAGAGCACAGGAAGGTCAAGATAGATACCAAACAAACCCTTCGCTAGCTGCCAGAGTGCACAGTTCGGAGTGTGGGACTCCAGTAGTAGCAGGTGTCGGAGGGCAGGAAAGGTTCTGTTATTTTCTTCCTTGATCCCCACGGCCCTTTGTGTTTTCATGTTTTATCTGTGCACTAATGGGCCAACACGTTGCTTCCTATCAGTTGCCTTCTCTGTTCTGTGTTGAGATGCTTTCCCTTCGCCTGTGCTGCTTCTCTGTGCCTTGCACTTAGTCACCCTTGCTTCTGAGAGGGTCCTGGGTCTTTCAGCCTGACTGTCCCCAAGCCATACTGTGTCTCACTGTAGTCTGACCTAGACACTTCTAATGCCAAAGGACATTAGCAGACCACAGTCAGGCTACCGGGTTGCTTGCTCTGAGGGTTTTATTGGGTGGAAAGCTGGGGATTATTATGTATTTTGAACAGAGAAAGTATAAATGTGCACGATGAAACATAGCTTCAAGTGTAAGTTTCAGAGCGATTTACTTAGCTACTTTATTATACTTCTCTCTGTTGTCCCACTGAAATGAATATTTACCTCCTCCCCTTACTGAGTCATAGACACTGGAAGTAATAAAACGGATGGTATTGCCCTCCAGACTTCTGGAGAAACTAGGTTCTCTGCTGCCTTCTTGGCCTTCAAGGTGCATATGTTGCCATACTAATCAGAAAGATTACAAAAACAAATACTAATAGACATTTAAGTATCTTAATTTTCTATTTCCTGTTTCCTGTTACTAAACACAGGGTTTCTGAGCAAGCATTTGGTTATTTTGGACAATCCTGCTTTAAAAATTAGATTCTAAAAAGACCTTTTATGAGAGTACATATAATAAATAAAGATGTCTATTAATTTCTTAAAAATCTAAATCCATTTCCTTTATGTTTTAAAATGTTTTCCTCATTATTTAGACAACTTTCAATTCTTCTGAAAATTTCAGTGTTCAGAAGCTGATTTTTAATTCTCTATCCAAAGAGCCCTGCCTCTAATAACTATAGTAAGGAATTATGCTGCAATTCTTGTCTCACTTGATTCCCATAGTCTTCTGTTCCAGTGTTCCTTCTCTGGAGTGCACTGACCATTTATCCAGGTATTTCTGATGTGAATAGGATGGGGATACCCTTGCTTAAAGTGTCCAAGGATGACCCAGCAGTTCTCTATACAACTCCCACTGAATTAGACCTTCTAAGAGTGTGTTAGGTCCCTGTTGTTCTGCCTTTTAGTGTATAGGTTACATGTACATGGAGAGAGAGTTTTTTTGTTTTTGTTTTGTTCTTTTACCAAGTGCTTAGGAATAGAGTTTATAGCTTTATATTTAAACTTCATCTTGCCTAATTAACCTTCACTTAAAGAAAGTAATGTGAATATAAAGATACCCCAATACACACACACACACACACACACACACACACACACACACACGTTGTAATTTCAAGAACATTGGCCAGAAACTTTCATTCTGATATCTACATGTCTGTCTGCTAATCATTTCTGTGTATTTAGTATTCACTTAGCTGGCATTCTTAGAAAATTAGATTTTTTTTTAAGTGTTACAAGGAGTCCTCCTGTTCCAGACTCTTGGTGAAAATATCTTATAAAATTGTTTTCTTATTCTAGAAGAGTGAAGCCTTGTACATATTGCTGAGCTGCCTCATTATGACTAGTCATTTTAAGCATTGGTTATTGCACAATGTGCTTAGTAATGCAGGGATGCCACTAAGTAAACACTAGAGTTACCAGAAAACTTAGCTTACAGATTGATTAAGTCTGAAATAAATTTTTGTCTGATTTAAACAG
Seq C2 exon
CTTTAGTGCAACCACCATTGTCCATGACCCCTGAAGCTGTGAAAGATGTTGGATTTGGCAGCCTGGTTTTACCAAGTGGTTCTGTTGCTGGCAGTCTTGCTCCTTCAACTCTACCAGCTGGAAATGTTTTTAATCCTCCCAGTAAAGCAGAGCCTGAAGAAAAAGTACCTCACCTTATAGAGCACCAGATTCCTTCTGGTGAGAACACAAGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
-Rbm16:NM_134123:18
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:
ENSMUSP00000132196





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000076024
  



Associated events






Conservation


Human
(hg38)
chr6:154827241-154830921 
LOW PSI
HsaINT0138316
(SCAF8)
Human
(hg19)
chr6:155148375-155152055 
LOW PSI
HsaINT0138316
(RBM16)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr9:92867947-92870743 
LOW PSI
BtaINT0128935
(SCAF8)
Chicken
(galGal4)
chr3:49632639-49633252 
ALTERNATIVE
GgaINT0081300
(SCAF8)
Chicken
(galGal3)
chr3:52254164-52254777 
LOW PSI
GgaINT0081300
(SCAF8)
Zebrafish
(danRer10)
chr17:48859756-48859839 
LOW PSI
DreINT0131091
(scaf8)
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
  • 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"