Special

MmuINT0130765 @ mm9

Intron Retention

Gene
ENSMUSG00000070953 | Rabepk
Description
Rab9 effector protein with kelch motifs [Source:MGI Symbol;Acc:MGI:2139530]
Coordinates
chr2:34641087-34646175:-
Coord C1 exon
chr2:34646023-34646175
Coord A exon
chr2:34641249-34646022
Coord C2 exon
chr2:34641087-34641248
Length
4774 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TTATTTTCTCTCTGGACTAGAAG
3' ss Score
7.13
Exon sequences
Seq C1 exon
GAACACACCAGTGGGACACGGCCACCAGGGAGGGCCTCTTGCCTCGGTACGAGCATGCCAGCTTCCTTCCCTCCTGCTCTCCTCACAGCATCTGGGTGTTTGGAGGTGCAGACCAGTCAGGAAATCGAAACTGTCTGCAAGTCATGAGTCCTG
Seq A exon
GTGAGTAGACACAGGTTACTTTCTTTTTATCGCTGTGATGGGTTGAATGCGCTTGGTTCAGGAAGTGGCAGTATGAGGAGGCGTGGCCTTGTTAGAGTAGGTAGGGCCTTGTTGGAGGAAGTATGTCACTGTGGGTATGGGCTTTAAGACCCTCTTCCTAGCTGCCTGGTAGCAGCCTTCAGATAAAGATGTAGAGCTCTCAGCTCCACCTGTACCATGTCTCCCTAGATGCTACCATGCTCCTTCTTTGATGATAATGGACTGAACCTCTGAACCTGTAAGCCAGCCTTAATTAAATATTGTCCTTCTAAGAGGCATAGTGTCTGTTCACAGCAATAAAACCCTAACTAAGACAATCGCACACTATGAATGCAGTTACGTTACAGTACATTGAATTGCTGTTGCCCTAACTAACCTATTTTACTTTGCTGACCTCTTAGAAATAGGAATTTATGGATTTTTTTATTTGTGTGGCTGTGTGTGCATGAGAGAGAGATCGTATGCAGTCTGTGGTGTCCACGTGGAAGCCAGAGGATGACTGTGGAAATCAGTTCTCCCTTTTTACCATGTGGGGTCCAGGGATCAAACTCTCCAGGGTAGCTCTGGTTTCATAACCTGCTCTCTGGCGATGGAATTATAGGAGTGTTTCATGTCTGACGGGACTGAATTGTCTTTCGTGTCGAGTATGAAATTTCTTTGTAGTGTTTGAAAAGTATCTACTTGGGGCTGGTGAGATGGCTCAGTGGGTAAGAGCACCCGACTGCTCTTCCGAAGGTCCAAAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCACCCGTAATGAGATCTGATGCCCTCTTCTGGAGTGTCTGAAGACAGCTACAGTGTACTTACATATAATAAATAAATAAATCTTTAAAAAAAAAAAAAAAAAAAGAAAAGTATCTACTTAGACGGCCATTGAAGTGGTTTGAGTGTTTGTAACCCACCATGCCCTTCCTCTGTGGAATGCAAATGCTTTTAAAAAACATATTATTTTATTTTATTTTATGTATATGAATACTTTGCCTGCATGTATGTCTGTGTCCCAGGTGTATCAGTGTCCAAGGATGTCAGAAGAGGGAATCAGATCCCCCCAGAACTGGAGGTGCTAGGAACCAAAGGCTGTAGAAGAGCAGTGTTCTCATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCCCCCCCATCCCTAGCTGTCATAGATTAGAGCTCACTCTGTAGACTAGGCTGGCCTCGAACTCACAGAAACCCACCTGCCTCTACCTCCCTCTGTGCTGGGATTAAAAGCATATACCACCACTACTCTCTTTTCTTTTGTTTGTTGTCTGTCTGTCTGTTTTTGAGTCTGAGTCTCACTATGTAGCCCTGACTGGCTGGCCTAGAATTCTTTATGTAGATCAGTGTGGTCTCAAACTCTCAGTGATCCTCCTGCCTCTGCTCCTGAGGGCTGAAATCCAAAGTGAAAGGCAAGCATCGCCACTGTGGTGATGTAAGTGCTTTGAGGTCTTGTTCTTTGTTCATAGAGTCCAGAGCACAGTCAGGTATGAAGTAGACAGTGCCTTGACCTCCTCGCCTATGCTGGAGCCATTTGTCTGGAACCATCCTAGAGTATGATCATCACGCTGGGGCTGGTAGTACAGGCCTGATACCCCTGTTACTTGGGAGGCTGAGGGGGAGGGACCACAACTTCAAGGTCATTCTGGGCTAGCATGTGATGATTGACAGCTGGAATCAGGCCAGAAGAGTGCTTGCCTGGGGGGCAGGAGTCTCTTAGTTTGGTTCCCAGAACTTGGGGCAGAAATAGTTCACGAGTCTGTGCTTTGCCGTACACTATCCGTGAGCTTGAGCCAAGCCCCTCAATTCCTTCCTTTCTCTTTTCTGCCACATGGGATATCAGTCCTTCCCTTGTGACCTTGTTAAAGATTTCTTTTCTTTTTTTAATATTATTTATTTAATGTATATAAGTACACTGTCTTCATACACACCAGAAGAAGGCATCAGATCCCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGTACCTCTGGAAGAGCCATCTCTCTAGCCCCTGTTAAGGATTTCGATTAGGAGCTAACACTCGCTCTCTGGTATTGACCCAGACAGAATTTGGGAAGTGGAAATCAGTTCAGGAAGTCCATCTTTAAGAAGGTGGCATGGAGGGTGTGGGAATGTTGGGAGACCTGGGAAAGGGTTCCTGGAATGTTGGGAGACCTGGGGAAGGGTTCCTCACTCTACCGCCCAGGGCTAGCCTGGAACCAAGATTTCCCTGTCTTGGCTTCCTAAATGCTGAGTTCACCAGGGTGTGCTGGGACCCTGTCCTTTCGGTTCTGGGGGATGACATTTATTTAAAAACAGAACTAAACAGAAATCTACAGTGGTGCATGCCTATAATCCCAATATTCTGAAGGCAGAGGCAGGCAGATCTCTATGAGTTTGAGGCCAGCCTGGCCAGGCGGGGCTATGTAATGAAACTCTGTCTCAATACCATACAACAGAAACAGACTGGTGGAACCTGGGAAAGCCGCTGTCGGGGAAGCTGATTGTCTGCACTGTTCATTTGTCTTGTTTCACTGACAGAGTCTCACTAGAGAGTCAAGGCTCTCAGTCTCCCTGTCTCATTCTACACTTACAAGTTTGAGCCACCAGACCCTGTTTGACTTTCCGTTCCTGGGCTCCAAGCCCTGCCCGATATCTGCAGCTCTAGAGACATTTCCTTTTGCTTTGATGTAGTGCAAGGCCCATTCTGCACTTGTGTTCCTGTTTGGCTCCCACATGCATTGCATGAGCCTTGGGTAGCATTTTGTGTGTTGAATGAAGAGTCTTTACAAAAGGCACAGTATTTCTAGATAGGAAATAATAGTCGATTTGGTGGGACTCTGACAGATCTGGCTTCAAACCTCACCTCTTCTCTCCAGAAGGCCTGTTAAAATGTCTGACCTTCCACACATCTCTCAGGGGTGAGTGGGAACCATGGAGGGACAGAGCTTAAGTTTTATTTTAAAAAGAAAGAAACTTCTTTACGCCCGTCATGTGGTGAGCTTTTGATTTCAAGACAGACTGGTAGAACATACACAGACCATGGTGTTATTATAACTGTTCAAACCTGGGCTGGAGAACTGCTCTGACAGAGGACCCAGGTTTGATTTCCAGTGCCCACATAGAGGCTCACAGCTGGCATAACTCCATTCCAGGGACCTACCACGCTCTTCTGGCCTCTGTGAACAACAGGCATACACATGGTGGCACATACATAGATGCAGGCAAGACACTCACATAAGATAAAATAAATTTGTTTTTAAATGTGTTTAAAAGCTGGAGAGATGGCTCAGCAGTTACAAGTACTAGCTGCTCTTCCAGAGGACCTGGGTTCAATTCTCAGCACCTACATAGCAGATCATAGCTGTCTTTAACTCTAGTTCCAGGGGATCTGATACCCTCACAGAGACACACATGCAGGCAGAACACCAATGCACATACAAAATCAAAATGAATTTTTAAAATGTATTTAAAGTCCAACAGCCATTTGCTAGCCGACTGTTAAGGAAGTAACAGTCTAGCTCGGCTTCAGCTCCAATGTGAGAAGGGAGAGACTGGCATTTATTTCTCATTTCTCATTCAGTTGGTTATCAGTAGTACCTCTAAAAGTGCAGTGAGGTTGCTGCTATCTTTCTTATTTTATTTTATTTTATTTTATTTTATTTTAGTGGTTTATATATATAAGTTCTTTATTTGTACCTGCACAGCAGAAAAGAGCATCAAATCCCATTACAGGTGGTTGTAAGACTCCATCTATAATGTGGTTGCTGAGAATTGAACCCAGAATCTCTGGAAGAGGAGCCAGTGCTCTTAACTACTGAGCCATCTCTCCAGCCTCATCTACTCTCTTTCAATGGCCACATTTTCTAGGAAGTTTGGCCCGTTTGGACTCTAGCATCCAGTGGGAGTGGATGTTAGCAGGCGTTGGACTCCTGCAAGCACAGAGCCGTCAGCACAGTGGATCCGCACTCAGACACGCTCCTGACCTCACTCCTAACTCAACCTGTGGCTTCTTAACTTTGGGAATTTCACCTGTCTGAACAACCTCTAATATCATCTTGGTTTTTTTTTTTTTTTAATGGTTTTAAAGCATTTATTGTAGAAAGGCAGAAAGAAGGAGAAGAGTAGAGAAGTAGAGGCCGGCCATGACCATGTGGAGAGAGGGGAGAAGGAAATGTGGAGAGAGAGGGGGACAAGGGAGCAAGAGTAAGAGCCAGGGAATAAGAGCTCTAATATCATCCTGTGCTTGCTCGGCACTGGAGAGTATGAGATCCCTGCCTAATGCTGTGCTGTGCTCTGCTGTGCTGTGTTGTGCTAAGCTGTGTGTGCTGAGCTGTGCTGCGCTGTGCTCTGCTCTGCTCTACTGCACTGTGTGTGCTGTGCTCTGCTGTGTACTGCACTGTGTTGTGCTGAGCTGCGCTCTGTGTGCTGCACCGTGTGCTGTGCTGTGCTGTCTTATACTGTTTTGTGTTCCTCAGAGACTCAGGTACAAAGGAGACCCTGTCAAGGTCCAGGTCTGCAGAAGTGGATCAGTAGGAGACTGCAAGCCTAGCAGGCCCGGGGTACAGATCCCCAGCACCTCAGAAAACAAAGAGTAAGGACAGAGCCTTAAGCCTAGGTCTTTTAAATGCTTATTTTCTCTCTGGACTAG
Seq C2 exon
AAGACAGGACGTGGAGCACACCAGAAGTGACTGGCTCCCCTCCATCCCCAAGAACATTCCACACATCGTCCGCAGCTATCGGAAACCAACTATACGTCTTTGGGGGAGGAGAGAGAGGTGCCCAGCCTGTGGAGGACGTGAAGTTGCATGTATTTGACGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000070953-Rabepk:NM_145522:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.340 A=NA C2=0.436
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0764610=Kelch_2=PD(20.8=21.2),PF134151=Kelch_3=PU(46.9=44.2)

							
A:
NA

							
C2:
PF0764610=Kelch_2=PD(20.8=20.0),PF134181=Kelch_4=PU(70.4=69.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000122360





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000037746, ENSMUSP00000113099, ENSMUSP00000120887
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:125213523-125220538 
ALTERNATIVE
HsaINT1028726
(RABEPK)
Human
(hg19)
chr9:127975802-127982817 
HsaINT0136374
(RABEPK)
Rat
(rn6)
chr3:13852343-13855894 
ALTERNATIVE
RnoINT0123388
(Rabepk)
Cow
(bosTau6)
chr11:96104124-96107927 
LOW PSI
BtaINT0121559
(RABEPK)
Chicken
(galGal4)
chr17:9589308-9589440 
ALTERNATIVE
GgaINT1023199
(RABEPK)
Chicken
(galGal3)
chr17:10311418-10311435 
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"