Special

MmuINT0075493 @ mm9

Intron Retention

Gene
ENSMUSG00000073421 | H2-Ab1
Description
histocompatibility 2, class II antigen A, beta 1 [Source:MGI Symbol;Acc:MGI:103070]
Coordinates
chr17:34401706-34404562:+
Coord C1 exon
chr17:34401706-34401978
Coord A exon
chr17:34401979-34404280
Coord C2 exon
chr17:34404281-34404562
Length
2302 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGC
5' ss Score
7.43
3' ss Seq
TGTCTTTTCTGTCACCCTAGAAC
3' ss Score
9.04
Exon sequences
Seq C1 exon
GGCATTTCGTGTACCAGTTCATGGGCGAGTGCTACTTCACCAACGGGACGCAGCGCATACGATATGTGACCAGATACATCTACAACCGGGAGGAGTACGTGCGCTACGACAGCGACGTGGGCGAGCACCGCGCGGTGACCGAGCTGGGGCGGCCAGACGCCGAGTACTGGAACAGCCAGCCGGAGATCCTGGAGCGAACGCGGGCCGAGCTGGACACGGTGTGCAGACACAACTACGAGGGGCCGGAGACCCACACCTCCCTGCGGCGGCTTG
Seq A exon
GTGAGCGCGGCGGGTCCCGCGGGAGCGCGGCGGGCCGTGAGGGGACGCGGAGCAGAGTTCCCGCCTGAGGAGCTGCATGGCCTCCTTCCTCCCGTCTGCCCTGCACCACCTAGCGCCTCCTTGGAGTCTCCCTCCTGTCTCACCTCTGCCCTCTGCCCTTTGCCTCATGAGGCCCAGCTGCCCTCTGACCCCTGGCTCTGCTGTGACCTCAGGCCCCTGTCAGCGCCAGCTCAGGGAGGCTAAGCAGGGGAGAGGGCGCCCGGGTGAGCGGCCAGGGTCCTGTCAGAAGCGGTTTAGCGCGGTAGCTCTGGCGTCCTGTGGTTTCTCCCCGCCATTCTGTTTTCCTGATTTCCGTGTGTTCCTTGAGGGCCACGGTTGTCTTGTGAGGGCTGTTTGCTGCCTGGCGCTGACCCGAAGGCATCACTGTCATTTCCCTCGTTCTCTGAGGGAGACTGTGTTGACTTGGGGCCACACTAAAAGATTCTGATACAAAATCTGAGGAACTCATTTCCGTTTCCAGCACACTCCCTGATACCCCCAGAGCCTCTCACCCGTGATGCCAATTAAAGTGGTCGGTTAGGCATCATATTCAGATCTAATCTCCTACATTAGGACTAATGCTTAACTCCAAAGGTTGCTTAAGTTTTCCCTTTTTACTTTCTGGGTGGCCTTGTTATTCAACGGTCGCAACTGATTCCTCACAGCAAGGGAACAGTGACCGGCCACCAGGAATTAATGATCTTGACTGTGGAGGAAAAAACCCCCCAAACCAAAAAACCAACCAAAACAGTTGTAGAGAGTAGAAAACGAACATTAAACAAGTTAAGTATGTATGCTGTTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCTCTCTTTCTCTCTCTCTCTCTTTCTTTCTTTCTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTCTTTGTTTTTTGTTTGTTTTTTTTTTGTTTGTTTTGTTTTTTGTTTTTTGGAGTCAGGGTTTCTCTATATAGCCCTGGCTGTCCTGGAACTCACTCGGTAGACCAGGCTGGCCTCGAACTCAGAAATCCACCTACCTCTGCCTCCCGAGTGCTGGGATTAAAGGTGTGCACCACCACTGCCCGGCGAAACATTTTATTAGATATTTTCTTCATTTACATTTCAAATGCTATCCCAAAAGTCCCCTATACCCTCCTCCCCCGCACCGCCCTGCTCCCCTACCCACCCACTCCCACTTTTTGGCCCTAGCGTTCCCCTGTACTGGGGCATATAAAGTTTACAAGACCAAGGGGCCTCTCTCCCCAATGATGGCTGACTAGGCCATCTTCTGCTACATATGCAGCTAGAGACACGAGCTCTGGGGGTACTCGTTAGTTCATATTGTTGTTCCACCTATATGGTTGTAGACCCCTTCAGCTCCTTGGGTACTTTCTCTAACTCCTCCATTGGGGGCCCTGTGTTCTATCCTATAGATGACTGTGAGCATCCATTTCTGTATTTGCCAGGCACTGGCATAGCCTCACAGGGTCCTTTCAGCATAATTTTGCTGGCATATGCAATAGTGTCTGCGTTTGGTGGCTGATTATGGGATGGATCCCCGGGTGGGGCATGTATGCTGTTTTCAATTTGAAGGGATAACAGCACTTGGCAAGAAGGCTTCTGAGGTAGTGGGCACAATATATCAAAGTCAGTCGAGAAACACTTGTGTCTGTGCACAACAGTCTGAGGGATGAAGGAAGAATGTCGCATTGCAGTCATTTTTGCAATTCCCCCCCCCCAAATTATTAACTTGAAATCGGAATCAATTTTTCTTTTGTCTTGTTTGTTTGCTTTATAAAGACAATTTATTTTTGTATTTAGTTTAAATAAAAATATTTTATTTACACATAAATTAAATACACAGTGGGTTTACAAAGAAGGTTTGTGTCAAGTCCTGGCTGTCCTAGACCTTGCTCTATAGGCCAGGCTGGCCTTGAACTCATAAGAGATCCTCCTGGCTCTAATTCCTGAGTGTACCACCACCTCCCGGCTTCTTTTGTCTTACTACATTTCACATTGTATGGGAACAGGGCCACAATGTTATTTTCCCAGTGAGTTAAGTTTGTATTTGTGGAGTTATTCTTCATTCACTGTTAGAACCTAGGCATTCATTCCCACCCTGCCTCTTCCCCAGGGGAGTCTCCACATTGCCTCACATTTCACTCACTGTCTTTTCTGTCACCCTAG
Seq C2 exon
AACAGCCCAATGTCGTCATCTCCCTGTCCAGGACAGAGGCCCTCAACCACCACAACACTCTGGTCTGCTCAGTGACAGATTTCTACCCAGCCAAGATCAAAGTGCGCTGGTTCCGGAATGGCCAGGAGGAGACGGTGGGGGTCTCATCCACACAGCTTATTAGGAATGGGGACTGGACCTTCCAGGTCCTGGTCATGCTGGAGATGACCCCTCGGCGGGGAGAGGTCTACACCTGTCACGTGGAGCATCCCAGCCTGAAGAGCCCCATCACTGTGGAGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000073421-H2-Ab1:NM_207105:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.100 A=NA C2=0.046
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0096914=MHC_II_beta=WD(100=81.5)

							
A:
NA

							
C2:
PF0765410=C1-set=WD(100=87.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000041008





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000109834, ENSMUSP00000129060
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr6:32487429-32489681 
LOW PSI
HsaINT0076466
(HLA-DRB5)
Human
(hg19)
chr6:32630026-32632574 
HsaINT0076454
(HLA-DQB1)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr23:25377423-25384782 
LOW PSI
BtaINT0026370
(BOLA-DQB)
Chicken
(galGal4)
chr16:102786-102871 
ALTERNATIVE
GgaINT0123424
(BLB1)
Chicken
(galGal3)
chr16:70418-70503 
ALTERNATIVE
GgaINT0123424
(E2JF30_CHICK)
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"