Special

MmuINT0026166 @ mm9

Intron Retention

Gene
ENSMUSG00000000202 | Btbd17
Description
BTB (POZ) domain containing 17 [Source:MGI Symbol;Acc:MGI:1919264]
Coordinates
chr11:114651983-114655440:-
Coord C1 exon
chr11:114655164-114655440
Coord A exon
chr11:114653837-114655163
Coord C2 exon
chr11:114651983-114653836
Length
1327 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAT
5' ss Score
7.79
3' ss Seq
CCTCTCCAATTCCCTTCCAGGTA
3' ss Score
11.47
Exon sequences
Seq C1 exon
CTCAGAGAGCCGATGTGGGTGGGGAGGCAGCAGGCACCGCCATCAACCACTCCCACATGCTGCTCCAGCGACTGCAGGACCTGCTGCGCCAGGGCAATGCCAGTGATGTCATCCTGCGGGTCCAGGCTGTGGGCACCGACGAGGTCCGAGCCTTCCACACCCATCGCCTGTTGCTGGGGCTGCACAGTGAGCTGTTCCGGGAGCTGCTGAGCAACCAGAGTGAGGTTATGCTGCGGGAGTCCCGGGACTGTGCTGCTGTCTTTGACAAGTTCATCAG
Seq A exon
GTACATAGGGGAAGGGCACCGTCCTGCATCCTGTCCTGCATCCTGTCCGTGGCTCCCTGTCTCTCCACCTTCAGGGGCGCAGAAGTCTGGCCTTACTGGTTATTATATCGACTTTCAAAAGTCCTAGCATGACATACAACACAGGCTTCCTTTATCCCTCCTTCCGATGCCCTCCCTGTTGTGGCCTGTGTCCCTTTCTGGCCTTTGGGAGTCCCTTCTGAGCTACTTCCAAACCCAGCCAAGAGCACTGATAGAATCAACAGATTCTTAGTTGGTCCCAAGTGTCTTCAATGGCCACAAGACTTTGAAACCACAGGGCTAAGGAGCAGAAAGGTCAACAGGCTCGGTCACCTCTCTCCTTCTTGCATAGGGAAAGACTGTAAAATGCTCTAAGGAGGTAACCCCGCTCTAAGGGCTCAGACAAGGTGGCTGCAGGATTCCAGACAACACCCCCAAGTTCCAGGCAACAGGAAGAGGGATAAAACAGAAGGGTTTCACATAGAGCCAAGCGGGGTGCTGTGTGCCAGTGGGACTGTCAGGAAGAATGAGGCAAGGGGGTGGGCAGCACTGTAAGAGAGCCAGGGACAGTAAAATGGCTGAGAGGGAGAGGGAATCCAGACAGCTGAAAAGCCTAAGCAAAGAGAAGCCGACAGGGAACAGGAAGTAGCCTGGGTTGCCTGTGTGCTGTGTAACGAGATTTTTTCTGAGCCTCTCACAGTGACAACATTCTGGAGGTGGGCTCTTCCCCTTTCTTAGGCATCTTGGGATTCCTAAATTAAAGGACTTGCCTTCTCTAGCAGCAAGGAGGAAGTCAGATAGGCATCTAAATCCAGACTGTGTGGATACCAAGGTTACTGGCGGCCTCTTATGGTTTGAGCTTAGAGTTAGCTATGAAGTAGATGCTTAGTAAATACATGTGATTTTCACAGCACCAGAAGCTAAAGATGTCTGAACAGGCCAGGAGGGAACTTAAGAAGAAAACATAGGAAGCCTCAAGGTCCATTCATCCTGTTTGTTTCTTACAAAAATGGCTGTGTCCCCTTTGGGTTCTGGGGAAACTTGCAAGGGTAGTGTGGGTGGCCTTGACAATACTCAGTCCCGCCGATCTTCCTATCTCTAATTTTTTAAATCATATTATTAGCATGTGTGTCTGTATGAGTGTATGCCACATGTAAATGGGTACCCTGCTCCAGCCAGAAGAAGGCTGGAGTTACAGATGGTTTCCAAGGCACCCAATGTGGACTCTGGAGCCCGAACTCTGGTGCTCTGGACAAGTGCTCTTAACTGCTGTGCCCTCTCAGCGGGCCCCTCTCCAATTCCCTTCCAG
Seq C2 exon
GTATTTGTACTGTGGTGAGCTGACTGTACTGCTGGCCCAGGCTATCCCGCTGCACAGGCTGGCCACCAAGTACCGAGTAGCATCCTTGCAGCGAGGCGTGGCCGACTACATGCGCGCACACCTGGCGGGAGGCGTGGGCCCCGCTGTGGGCTGGTACCACTACGCTGTTAGCACCGGGGATGAGGCTCTGCGCGAGAGCTGCCTGCAGTTCCTGGCTTGGAACCTTTCTGCCGTGGCGGGGAGCGCGGAGTGGGGAGCCGTGAGCCCCGAGTTGCTGGCGCAGCTCCTGCAGCGCTCGGACCTGGTGCTGCAGGATGAGCTGGAGCTGTTCCACGCGCTGGAGGCGTGGCTGGGCCGCGCGCGGCCGCCCCCCACCGTGGCCGAGCGAGCGCTGCGCGCCATCCGCTACCCGATGATTCCGCCTGCACAGCTTTTCCAGCTGCAGGCGCGCTCGGCCGCGCTGGCGCGCCACGGCCCGGCGGTGGCAGATCTCTTGCTGCAGGCTTACCAGTTCCACGCCGCCTCGCCGTTGCATTACGCCAAGTTTTTTCACGTGAACGGCAGCGCCTTTCTGCCGCGCAACTACCTCGCCCCAGCCTGGGGCGCCCCGTGGGTCATCAACAACCCGGCTCGCGACGATCGCAGCACCAGTTTCCAGACGCAGTTGGGACCCAGTGGTCATGACGCGGGTCGCCGGATTACCTGGAACGTGCTCTTCTCCCCGCGCTGGCTGCCCGTCAGCTTGCGGCCGGTCTACGCGGACGCCGCGGGCACCGCGCTGCCTGCCGCGCGCCCCGAGGACGGGAGGCCGCGACTAGTGGTCACGCCAGCTAGCAGCGGTGGCGATGCGGCGGGCGTGAGCTTCCAGAAGACAGTGCTGGTGGGTGCGCGCCATCAGGGCCGCCTCCTGGTGCGCCACGCCTACAGCTTCCATCAAAGCAGCGAAGAAGCTGGCGACTTCCTGGCCCACGCAGATCTGCAGAGGCGCAACTCGGAATACCTGGTGGAGAATGCGCTGCATCTCCATCTCATTGTCAAGCCGGTGTACCACACCCTCATCCGGACTCCCAGTTAACCTCTGGATTGAGAAATAAGGCTAGGCCTGGATGGCGCACCAGGGTGTCAAAGTGACTGTTGGCCCGGGCCTTGGGTGATCAGGTGCAGCCGGTTGGGACTAGGGTGGAAGGCAGGTGAATGTGGTAGACAAAATGGCTGTGGTTTCAGGAGTGCCTTCTCCAGCTAATTTGAAGGCAGCATTCTTGGTACAGAATAAACCGATGCTCAGAGGGGCCAGGTACTGAAGCAACTCCCGGGTCTCAAAAAATGTCTGGGGTTCACATACCCTCCACTAGCTCCTCCCTGCCAGACACCCCACCTGGACATCAATTAGGGCGGGGAAGATTGATTGCCAGGGCTTTGGTCCTGGCAATCTCCCTCTTGGATAGGAACTTCCACATTTGAGCCGAGGTGCTCTCTGAGCTGCAGTCTCCAGGGGGCAGCAGCCCCTGTGGCTTGTGGGACATTCTGCCACTGCCCTTCAAGTCCCTGGCCTTAGTGAAGGGTCCAGGGTAGTGGAAAGGTCTTGAGAGAGGGCGGAAAACTAGACCTAGCTCTAGCCCCATTTTTTTCTGGAGAGGGAGAGTCTTGGCAACTTGAAGAAAAAACATTCCCCAGTTGTGTGTAGGTTTGGGCCATGGGAGATGAGGCTCTGGGAGAGAAAGGGCCAGGATCTGGACCAGTCTGAGTCCCCACGCTGCACATTCCACAGCTCCCAACACAGCCGTCAAAACCCCAGTAGGACTTTATTTGAAAGAAAGGCAAAAAGAAAAAAAAAAAAAAAGCAACAGAGAAGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000000202-Btbd17:NM_028055:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.078
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0065126=BTB=PU(61.8=73.1)

							
A:
NA

							
C2:
PF0065126=BTB=PD(37.3=11.4),PF0770710=BACK=WD(100=28.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000000206





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr17:74357732-74359968 
LOW PSI
HsaINT0018986
(BTBD17)
Human
(hg19)
chr17:72353871-72356107 
LOW PSI
HsaINT0018986
(BTBD17)
Rat
(rn6)
chr10:103336255-103337495 
ALTERNATIVE
RnoINT0026888
(Btbd17)
Cow
(bosTau6)
chr19:57719765-57721367 
LOW PSI
BtaINT0027257
(BTBD17)
Chicken
(galGal4)
chr18:9404382-9404695 
ALTERNATIVE
GgaINT0128453
(BTBD17)
Chicken
(galGal3)
chr18:9152440-9152753 
ALTERNATIVE
GgaINT0128453
(BTBD17)
Zebrafish
(danRer10)
chr12:36403224-36407988 
LOW PSI
DreINT0038567
(btbd17a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
ATGCCAGTGATGTCATCCTGC

				
R: 
TAACAGCGTAGTGGTACCAGC

				
Band lengths: 
351-1678

			

		

	





	
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"