Special

MmuINT0176620 @ mm9

Intron Retention

Gene
ENSMUSG00000079243 | Xirp1
Description
xin actin-binding repeat containing 1 [Source:MGI Symbol;Acc:MGI:1333878]
Coordinates
chr9:119922873-119928937:-
Coord C1 exon
chr9:119925544-119928937
Coord A exon
chr9:119925153-119925543
Coord C2 exon
chr9:119922873-119925152
Length
391 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
TCCCCCTCCTACTCTCCCAGCTG
3' ss Score
8.5
Exon sequences
Seq C1 exon
AAGGATGGCTGATGCCCAGATGCAGGTAGCTCCTACACCAACCATCCAAATGAGGACAGAAGAGGACCTGTCCCTCCCTCATCCCTCAGCCCCAGAGGGTCTGCCGCCACCACCCCCCAAAGAAACCTTCTCCAAGTTCCAGCAGCAGCGGCAAGCCAGTGAGCTCCGGCGTCTCTACAAACACATCCACCCTGAGCTTCGGAAGAACCTCGAGGAGGCTGTGGCTGAGGACCTGGCGGAGGTCCTCGGTTCGGAGGAGCCCACTGAGGGCGATGTTCAGTGTATGCGCTGGATCTTTGAGAACTGGCGGCTAGATGCCATTGGCGATCACGAGAGGCCGGCTGCCAGGGAACCTGTGTCAGGTGGCAACGTCCAGGCCACCTCTCGAAAGTTTGAGGAAGGCTCCTTTACCAACAGCTCAGATCAGGAGCCGGAGGGACTCCGGCCATCAGGGGGTGATGTCCAAGCTGCCAGACAGATGTTTGAGACCAAGCCACTGGATGCGCTGAGAGGCCAGGAGGAGGCAACACAGACAACCATGAGGGAACCTGCAGCCACTGGAGATGTACAGGGAACCAGAAAGCTCTTTGAGACTAGGCCCCTGGACCGACTGGGCTCCCGCCCCTCTATCCAGGAGCAGAGTCCTTTAGAGCTGCGCTCAGAGATTCAGGAGCTGAAGGGCGATGTGAAGAAGACGGTGAAGCTGTTTCAGACGGAACCTCTATGCGCCATCCAGGATGCCGAGGGCACCATCCACGAAGTCAAGGCTGCCTGTCGGGAGGAGATTCAAAGCAATGCAGTGAGGTCTGCTCGCTGGCTCTTTGAGACCCGACCTCTGGATGCCTTCAACCAGGACCCCAGCCAGGTGCGGGTGATTCGGGGGATCTCCCTTGAGGAGGGAGCCCTGCCGGATGTCAGTGCAACTCGTTGGATCTTTGAGACGCAGCCTTTGGATGCCATTCGTGAGATCGAGGTGGACGAGAAGGACTTCCAGCCATCTCCGGATCTCATCCCTCCTGGCCCAGATGTTCAGCATCAGCGACATCTGTTTGAAACCTGTTCCCTGGACACTCTGAAGGGTGAAAGAGAAACAGAGGCAGAGGTGCCACCCAAGGAGGAGGTGATTCCTGGCGATGTCCGCTCTACACTCTGGCTATTTGAAACAAAACCCCTGGATGCTTTCAGAGACCAGGTCCAAGTGGGTCACCTGCAACGGGTGGGTCACCAGGAGGGTGAGGGGCTTGTGACAGAGTGTCTACCCAGTAATGGTACTTCGGTGTTGCCTCTGTCTCAGGGTGTCCCCCAGAATGATGGGTTGAAAGGGGATGTGAAAACCTTCAAGAATCTTTTTGAGACCCTTCCCTTAGACAGCATTGGGCAGGGTGAGCCTTCAGCCTATGGGAACATAAACAGAGGACAAAACACTGATTCTGCCGAGCAGTCCCAGGGTTCTGACGCCCCGGTATATGCTATGCAGGACAGCAGGGGACAGCTTCATGCCCTGACTTCTGTCAGCAGAGAGCAGGTAGTTGGAGGTGATGTTCAGGGCTACAAGTGGATGTTTGAGACACAGCCCCTGGACACGCTGGGTAGAAGCCCCAGTACCATCGATGTGGTACGAGGTATCACTCGGCAGGAAGTGGTGGCTGGGGATGTCGGCACCACTCGGTGGCTCTTTGAGACGCAGCCATTGGAGATGATCCACCAACAAGAGCAACAGAAACCAGAGGAGGAAGAGGGGAAGGGTCCAGGAGGCCCCCCCCCTGAGCTCCCCAAAAAGGGTGATGTACAGACTATCCGTTGGCTGTTTGAGACCTACCCTATGAGCGAGTTGGCAGAGAAGCGAGAATCTGAGGTCACAGACCCCGTGAGCAAGGCTGAGACACAGTCCTGCACCTGGATGTTTGGGCCCCAATCTCTGAACCCAGCAGAAGGCTCTGGGGAGCAGCACCTGCAAACCAGCCAGGTTCCGGCTGGAGACAGGCAGACAGACAGACATGTCTTTGAGACTGAATCTCTGCCAGCCTCAAACCAATCCAGTGGGAGAAAGCCTGTAAGGTACTGCAGCCGGGTGGAGATTCCTTCCGGGCAGGTATCTCGGCAGAAAGAGGTTTTCCAGGCCCTGGAGGCGGGCAAGAAGGAGGTCCCGGAGACCACAATCAACCTGGGGTCCATCCCCACAGGCTCTGTGCATAAATTCACCTGGCTCTTTGAAAACTGTCCCATGGGCTCCCTGGCAGCTGAGAGCATCAGAGGGGACAACCTCCAGGAAGAACAGCCAAAAGGCTCTGCAGGCCATGGGACACCAGAGAGGCAGGAGACAGCAGCCGAGAGAACCCTTCGGACTTTGCATGCCACCCCCGGCATCCTGCACCATGGAGGCATCCTCATGGAGGCCCGAGGGCCAGGGGAGCTCTGTCTTGCCAAGTATGTGCTCCCAAGCCCAGGGCAGGGGCGCCCCTACATACGGAAGGAGGAGCTGGTGTGTGGTGAGCTTCCCAGGATCGTCCGTCAAGTGCTGCGCCGGACAGACGTGGACCAGCAGGGACTGCTGGTTCAGGAGGACACAGCTGGGCAGCTCCAGCTCCACCCACTCACGCTGCCAGGGCCTGGTGACCCTGGGAATATTGAAGACATGGACCCTGAGCTCCAGCAGCTGCTGGCCTGTGGCCTGGGAGTCTCTGTGTCAAAGACGGGGCTGGTGATGCAAGAGACAGGACAGGGCCTAGTGGCACTGACTGCCTACTCCCTCCAGCCCCAGCTTACCAGCAGGGCCCCTGAAAGAAGCAGTGTGCAGCTGCTGGCCAGCTGCATAGACAAAGGAGACCTGCACAGCCTTCACAGTTTGCGGTGGGAGCCGCCAACAGACCCAAGTTCTGGACCTGCTACTGAGGAGTCCCAGAGGGTCCCCCAAACTGAGAGCATCATACATGTTACCCCATTAGACTCCACCATGGAGATGGGGCAGCTGAGAATCTCAGGATCCACACCCTGCCCACCTCCATCTCGGGCAGCTGGAAAAGTGGTCCTTCCAAATGGGAAACCTGTAGCCCAAGCTCCATTGCAGGAAGCAAGGAAGAAAACGGATATCAGCCATGCTGGGCAGAAAGGGAAGGCAGCCTCAGGAAGACCAGAAGGAACCATTGCTTCCCCTCTAGGGTCTGGGGCTCCAGATCTCCAGGAAGCCATGCAGAATCTGCGTTTGGCAACCGCTGAGGCCCAAAGCCTGCACCAGCAGGTTCTGAGCAGGCATCCACAGGGCTCTGACCCTGTAGCCACCTCCATGCCTGTCCAAGATGTTCTGCAAGCATCCACTCCTGCCACTGGGGTTACTCAAGGCAGCATCAGGCCTGTGGCTGGAAGTGAAGCCAGGATCCCAGCATTCCCCAGAAAG
Seq A exon
GTCAGTGGGGACAACAAAGCAGTCCCCAGAGGGCTGCCTAGGGGGTGGGTGACCATACAGGATGGCATCTACGCTGCTCACCCTGTGAGAACCTCTGACCCACATGGGGCTATCCAGCCTTCTGAAAAAGAGCCCCATCTGAGGCACAGCCCACCCCAGGCAGACCAAGGTCAGAGTCCCAGGCCGGGGTATCGTGAGCCTGGGGGTCATACACAAAGGGCTTGGGAACCTCTGGGGAAAGTGATGCCCCAAATCTCGCTTGAGTGCCTCCGGGCAGCAGACACCTCCCTGAAGACTGCCCCTCTAACTCACCACACCCTGACATCTAAACCAGCAGGTGCCAGCCTGCACTCCCATAATGCCTCTGTTCCTCCCCCTCCTACTCTCCCAG
Seq C2 exon
CTGCTGTGACAGAAGATCCTGACCACCCAACTCAAGGCCACCACCAGGAGGACTCCATCCAGCAGGCCCCGGAGCCCCTGCAGGAACCCCTTCTTCATATTCACAACAGACCTTCTGGCCAGAAAACCCCTGAAGGGTCAGAGACAAAACCCTCCAAAGCGGAATCCACCATGCTTCCAAGAAAGAAACCCCCAGTGCCTCCCAAACCTGCACATCTAAGCCAAATCCACCCACCTCAGAGGCTGCCCAAGCCCTTAGCAGGCTCTGCCAGAGCCTCAGAAGCAGGACAAGACCATAAGCCAGGTGAGCCAGGTATAGCCAACCCAGGGTCAGACAAAGCTCCCACAATAGCAGGCCAGGACTGCCTGCCTCTGGCTGAAAGCTCCAAGGGCCAGAAGCAACCTGCTCATCAGCGTCCACTCAGCTCTATGGCTTCCAGGCCTAGCAGGGGTCAGATAACCAGCAGCAACAGCCAGAGCCCCGAGTCTCCTAAGTTGAACGTTCTCAACAATGACTCCAGCCCACCACAAAAGCACAATAGCTCCCCCCAAAAGCAGGGGACCCCTGAGAGTCCACAGGGCAGCCATCAGGAGCTCCAGGGCCTCCTGAGCCAAGTGCAAACCCTGGAGAAGGAAGCATCTCGCAGCGTGGATGTGCAGGCCCTGCGGAAGCTCTTCGAGGGCGTACCCCAGCTGGGAGGGGGAGTCCCTCAGGCTCCCACTGCCCCCCACATGACTGAGGCCTCCATGGAGCAGGCCTTTGGGGAACTGACTCGGGTGAGTACAGAGGTTGCCCAGCTGAAAGAACAGACCCTAGCCAGGCTGCTGGACATCGAAGAAGCAGTGCACAAGGCTCTTAGCTCCATGTCTAGCCTCCAGTCTGAGGCTCCCACAAGCAGCCATCCACAGGGAACTACAAAAGATCCCAGTGTGAACAAGGTCTCAGTCAGTAGCAGAGCCATACAGACAAGCTCCAGCCAGGTCAGAGATCCACCCCTCGTCAAAACCCAAGAAAAGGCCGAGAGCCATCCTGAGGACAAGATGAGAAATCACGCAGAGGCCAGAGGCCAGGCAGCAGTGAACGTCCTGCCCTCCAGGAGGCTGGAGACACTGAGAGGAGCCGAGCCTGGCCTCCTACAAGTCTCTCCTCCCTGCACAGGATCCTCCTCTCCAACTTTCATCTCAGTCCAATCAGCTACAAAGAAGCTTCCGGAAGCTTCTAGCCCTCAGGGAAGCCATTATATCTCAGGGAAAAATACACACCTAGGTCAGGACATAGGTCAAGCCCTGCTCTACCAGAGAGATATCCAGGATCAGGCTGGGACAAAGGAGATGTGCATCGAGGGCGCTGTGCTCACAGGGCAGCCAAAGAATGTTCTGGAATTCCAGACTGGGTCAACTACCTCCAAGTCCTATGGAGCCATGAGAACAGTGACCGAGCAGTATGAGGAGATGGACCAATTTGGGAATACAGTCCTCACTTCCTCCACCACCATCACCCAGCACGCAGACCCACTGACGGACCCCAGACCCCAGCTCTGCCTGCACACTTCTCCCATGCTAAGGCAGTTACTCCACAGCCCCTCCAGGCTCAACAGTGACCTGGCAGAAGCTGAGATAACATGGACTCCCTGTAACAACTTCCACCCGGCTGCCCAGTGAGCCCCTCTGTCTCCCACCAGTCTTGGGTACCTCTCCCAGAGCTCCCCCAGGACTGAGTCATGGGCCTACCTCCAGCACATGTGGAACAAGGACCAAGAAAAAAACGTGGCCTTCAGAGAGCTCACGAGGGCTGTTTGCCTTGTTAGTTCTTGGAAAAGAGGCAAGAAACATAAAGCAGCCATCCACAGGAAAGCCGGATGGGAGGGACAGGACCTGACAGGTGCTTGTGGAGAACTAGCCCACACTAGCCCAGCTCACACTCACACATGTGAGCCTGCACCTCATTGCCTAGAGCTGGAGGGTCACCCTGCACTGTGTCCCTCCATAGCCAGCCTTTTTCTTTGGTTATGGAATCTGGCTGCCTTAATCCCTGGTGAGGACCCGGGGCTGAGCAAACTGGACATGACACTGCTCTCTGTTTGAGATTGGACTAAAGGCTCCAGAAAAACCCGGGTGCCTGCCTCTTCATCGCCAGTGGTCCAAAGGGCGCAGAGAGCGCACTAGCAGTCAATAGTGTTCCGAGAAGCTGAATACACGACCCTTCCTGACCCCATCACCCCCACTCTGCACCCCGAATGGGAAAAAATGACCCAAAAATAAACCCAAAAGAGATTCCCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079243-Xirp1:NM_011724:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.675 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF080437=Xin=WD(100=1.4),PF080437=Xin=WD(100=1.4),PF080437=Xin=WD(100=1.4),PF080437=Xin=WD(100=1.4),PF080437=Xin=WD(100=1.3),PF080437=Xin=WD(100=1.4),PF080437=Xin=WD(100=1.4),PF080437=Xin=WD(100=1.4),PF080437=Xin=WD(100=1.4),PF080437=Xin=WD(100=1.4),PF080437=Xin=WD(100=1.4),PF080437=Xin=WD(100=1.4),PF080437=Xin=WD(100=1.4),PF080437=Xin=WD(100=1.4)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000107262





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr3:39227153-39227579 
ALTERNATIVE
HsaINT0183579
(XIRP1)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr22:12552081-12552462 
Chicken
(galGal4)
chr2:4947543-4948020 
Chicken
(galGal3)
chr2:4878359-4878836 
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CTCCAGATCTCCAGGAAGCCA

				
R: 
CTGGCCAGAAGGTCTGTTGTG

				
Band lengths: 
349-740

			

		

	





	
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"