Special

MmuINT0062053 @ mm9

Intron Retention

Gene
ENSMUSG00000054942 | Fam73a
Description
family with sequence similarity 73, member A [Source:MGI Symbol;Acc:MGI:1924567]
Coordinates
chr3:151998216-152001008:-
Coord C1 exon
chr3:152000690-152001008
Coord A exon
chr3:151998394-152000689
Coord C2 exon
chr3:151998216-151998393
Length
2296 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAC
5' ss Score
7.82
3' ss Seq
TGTTTAACTATTTTTTCCAGATC
3' ss Score
8.37
Exon sequences
Seq C1 exon
ACAGGGTCTCAGTATGTATCTCTGTCTGGCCTGGAACTCCCCGTGTAGACCACACTGACCTCAAACTCACGGAGATCTGCCTCCCAAAAACTGGAAGCAAAGGCATACAGCACCATACTCAGCAAGACTTCAACTTTGCATCTTTCATGGATAAAGCACCCAGAAATCCCTGTGGCTGATTAATTCCTGTTTCATTGATTTAAGATTGGACAGAGGCGACATGTCAGACGAGACAGTCAGCAGATCACAGTTCTCCTTGAAGACGTACGCAGTTAGAGTGTTTGCTCTCCCTGTGTCTTGGTATTATTCTCTCTCCCAG
Seq A exon
GTAAACGTCAAAGTGAGCTGAATTTGAATAATACCTCTATATTGTTCGGTAATGTTTGTTCACTTGAGGCTGTTGTTTTGTGGTGCTACGGATTTAAACCCAGAGTTTGCTAAGCAGGCTTACTGCTACTTAGCTACATTTCCCAGCCCCTGAGGTTTTCACACAGCACAGGGGACTGCAGTACTTTAAATAGTTTCCTTTCTTAGGCAGGTATGGTGACGTATGTTGGGTTATTGGGTGTTCCGTGTCTGCTTGGGGCTCAGGGAACTGCGCTTACCCCATTCCGGCACCGCCAGCATGGGGCCCCTGCTGGTCGGTTGGGTGTCAGGCTATGTGAAGCCTCTGAACCCCACTCCGGGGGTGGGGGAGCACAGTCTGAGGTCCCGGGAACTGCCGGAACTGTCTTGGGGGTCCCCTGGCCTGCCTGGAGACTGGAGGCGGAGACCATCTGGTTCTTAGGCTCTTGGGCACCCCAGGTGCTGCTGGAGGCCACGGAGGAGGTAAGAATAGAGTGGGGGCCTGTGGGCTGGATCTAGTCCTGGAGCCAAAGGAGAAAAGAGAGGGGAGCTCTGGCTGGGTTCTGCAGGGATAGAGTCCTTGGTTTGTTCGGCAACAGTTCGCTCGGCTTGGTGGAGGCCGTGTCTGGGAGTGCTGAGAGCCCTTCTGCGGGATTAGACGAGGCTCTTTGGAGGAAGAGCCATTGTTCAGTTCCATTGCTCCCCACAGTGGATCCCAATGAGAAGAGACAGTCCATGGTTTTAAGGCATTTATTGTCATGGAGGAGAGTGGCAATGAGTAAAACTGTACCCCAGTTTCTCAGAGCAGGCCTGAGGTTAAATACGTTTTGCAGGGAGGAGTGTCTGGAAAGGAGAGCTTAATTGGCTAAGTCCTTTAGGCCTTTAGGTGCCTCATTAAAATGGAGATCTGTCTTGAGGCTACTCCATCTATGGTCAGGTCCTCTACCCGTGGAGGGGCTTGGGGCGTTGCCTTTACGTGACTGATGGCCACAGAATTATGGAGAGCTGCATCCTTGGGTCAGGAGTCTAGTGCCCAGGAGCATGGCAAACGCCTGCATCCCTCAGGTTCACCGGGGTTTCCAGCCTGAGCTCGACCAGGAACCAGGCTGCCATTCACGGTCCTGCAGACATACACCTTTAATCCTGTTCCTGGCATTTTTATATCTGGTGTACTTTCCTGCGCATAAGAATCTTCAAGGCACATTGTAGCCTTGTAGCACACATTGGAATGCGCCTTTCTAAATGGAAGTAATATTCCACTGCGTATGGATATGTATTTCCATCCACCTGGGAGCTGTTTGTGTCGTTTCCGTGTTTCAGCCGTCTTGAGTGGTGCTTCTCTAAGCACGGAGACCTAACTAATGCTTTGATGTTTGTGCTTTTGGACATCCTGCTAATCCCAGCACTCCAGGTGGGGTGGGGGATGGGGCTGAGGAGATGGTTCATACTAGACCCAGATTTGACCTCCAGAATCCACATCTTAAAACAAAAAACAAGAATCAAGAAAGCCAGGCACAATGGGGAGCAATTGGGAGGCAAAGATAAGAAGAGCCTTAGTTCGAGCTTGTGAGCCCTGGCTTTGACTGGCTCGTCTGGCCAGATTAGTGAGCTCCAGGTTCAGAGGTGGACATTGGAGGGTGGGGGGCGACGGCTGATGTTTTCCTCTGTCCCCAAGTGCACACACAGAGACCAAAAAATCAGAGAAGAGGGAATGCCCTGCTTTCAGGTCTCTCTAGAATGATTTTTCAGAAGCAGAGTTTTTGAATCACGTTAGTTCCTTTCGTGTTTTCAGAGCTGCTGTGGTGTTTTCCACAGTCAGTGCTCTGATATATACTATAGTCTTGGCAGTGCCAAGTTACACTTGGCAGTTACACTGTGGGGGCTCCCCTGCAAGTATATCCTCTCCTGACCTTTCCTCTCATTCCATGGGTTGCTACTCTGTTGTTAGTATCTTTTATTCTGGTTTTAAAATATTTTTATTTTGCCTGTGCATATTATCTAGGCACCATGTGCATGCCTTGGTCTGTGGAGACCAGAAGAGCCCCAGCTTCTCTAATTGTCCAGATAGCAGGGTTCTAAAAATACTTTTTGATTATTTTTTGAATAAAATAACTATGCCTGTAGTATTTAGAAATAAATTAACTTTTATATTTGATTAAAATTCCAAACGTGTATCTTAAAAATGAGCCCAGCTTTAAAATCTGATTTAACTATTTCTGTAGTTAAAAAGACTCAGTTACATGGAGGGTTGTTTTGTTTTGTTTAACTATTTTTTCCAG
Seq C2 exon
ATCAAATTTTCACCAGTAGCTAAGAAGCTGTTCATGGTAACTGCCGTGAGTGCTGTGTCTGTGATTTTTCTGGCCCATCACTTTAAAAGAAGACGGGGAAAACAGAAGGGCAAAGTGCTGCCCTGGGAACCCGAGCACCTCCTCCTTGAGCACACTAGGAGAGCTGCATCAGAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054942-Fam73a:NM_174868:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.050
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF102654=DUF2217=PU(2.5=21.2)

							
A:
NA

							
C2:
PF102654=DUF2217=FE(21.0=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000072836





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000068261, ENSMUSP00000072836f4939A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:77783352-77801330 
ALTERNATIVE
HsaINT0061423
(MIGA1)
Human
(hg19)
chr1:78249037-78267015 
ALTERNATIVE
HsaINT0061423
(FAM73A)
Rat
(rn6)
chr2:257544895-257546700 
LOW PSI
RnoINT0092505
(Miga1)
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
chr8:17877959-17879252 
LOW PSI
GgaINT0039121
(FAM73A)
Chicken
(galGal3)
chr8:19678820-19680113 
LOW PSI
GgaINT0039121
(FAM73A)
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"