Special

MmuINT0094292 @ mm9

Intron Retention

Gene
ENSMUSG00000028649 | Macf1
Description
microtubule-actin crosslinking factor 1 [Source:MGI Symbol;Acc:MGI:108559]
Coordinates
chr4:123073156-123074663:-
Coord C1 exon
chr4:123074337-123074663
Coord A exon
chr4:123073241-123074336
Coord C2 exon
chr4:123073156-123073240
Length
1096 bp
Sequences
Splice sites
5' ss Seq
CTGGTATTT
5' ss Score
3.5
3' ss Seq
ATGCTCTTCTTTCCTTTCAGGCT
3' ss Score
11.34
Exon sequences
Seq C1 exon
GCTCTAGAGGAAGAAATAGAAAACCATGCAACAGATGTGCACCAGGCAGTTAAAATTGGGCAGTCCCTCTCCTCCCTGACATGTCCGGCAGAGCAGGGCATCATGTCAGAAAAGCTAGACTCATTGCAGGCCCGATACAGTGAAATTCAAGACCGGTGCTGTCGGAAAGCATCCCTGCTCGAGCAGGCCCTGTTCAATGCTAGGCTGTTCGGGGAGGATGAGGTGGAGGTGCTCAACTGGCTGGCTGAGGTTGAGGACAAGCTCAGTACAGTGTTCGTAAAGGATTACAGACAGGATGTCCTGCAGAAACAGCATGCCGACCACCTG
Seq A exon
GTATTTGTGTTTTCATTCTTATGTTACTGAATTATTTTGTCATTCTGATATGTGTTCCTTTTCATTTCTTTTTCTTTTAATTTCTTTTTTCCCCTTCATTCCAAACACTTCAGCTTTATTGTGTGCATAGAATATTTATACATATACATAGTTGAGTTGTTGCCAAGTACTAGTCCTTTTTGGATAGGTCCATGAATAAATACTCGTATTTAACAAGTGAACTAATGATTCTACATTATACAGGTAAGAGGCAGGTCCATCTCAGTTGCACATTGGGTAGGTACATCAATGGATCAGTAGGTTTTCATTTGAGTAGATGAGAGCATTCTGTAACGAAACCACATATATCTGAATGGTGTCCATAATCTCATCGTGTACTTGTAACTTAATATTTGTGAAATCCAAGACATTCTGTATTGTCTTATACAATATGTCTGTTTTGATTTTTTTTAAAGATTTACTTATTTATTTATTATATGTAAGTACATACACTGTAGCTGTCTTCAGACTCTCCAGAAGAAGTTTCAGATGGTTGTGAGCCACCATGTGGTTGCTGGGATCTGAACGCAGGACCTTCAGAAGAGCAGTTGGCGCTCTTAACCACTGAGCCATCTCTCCAGCCCTTGATCTTTTTTCAATTATGTGTCTGTGTGTATATGTGCATGTCAGATCTGTGTGGACGTGGAGGCTAGCTGCCTCGTGGTGGTGGAAATCAAACTCAGATTCTCTGGAAGAGCAGTCCCTGTTCTTCACTCCAGCCATGTTTTAGTTTGCTTCATGAAGTCTATTTTAGACACAACGCGCATTTTTGATGTATTTCCTTTCTAAACTTCTTGTGTTGGAGTTTGATATCGGTTGATTGGTAAAGCCGATTTCACCCTAAATCTTTTCCATCCAGCATGAAAGAGAGCTTGCCTATAGAGCATTTCTTAGTTGTCTTTAGCAGAGTAACCACAGAGATACAGAAAGGAATCAACTATCTGACTTTAAACTGAGCTGCTAATGGATCTCTTTAGGTGTTGTCCTTTTAAAGCGCTCAGAGTGCTTCCCTTTCTTATGCCATAGATTTGAAATTAATGCTCTTCTTTCCTTTCAG
Seq C2 exon
GCTTTAAATGAAGAGATTATTAATAGAAAGAAGAATGTAGATCAAGCAATAAAAAATGGTCAGGCTCTTCTAAAACAAACTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028649-Macf1:NM_009600:57
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.009 A=NA C2=0.078
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0043516=Spectrin=PD(57.0=56.0),PF0043516=Spectrin=PU(40.6=39.4)

							
A:
NA

							
C2:
PF0043516=Spectrin=FE(26.2=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000101819





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000095509, ENSMUSP00000114568
  



Associated events






Conservation


Human
(hg38)
chr1:39428288-39429241 
ALTERNATIVE
HsaINT0098150
(MACF1)
Human
(hg19)
chr1:39893960-39894913 
ALTERNATIVE
HsaINT0098150
(MACF1)
Rat
(rn6)
chr5:141085388-141086341 
LOW PSI
RnoINT0088184
(Macf1)
Cow
(bosTau6)
chr3:107228203-107230113 
LOW PSI
BtaINT0088427
(MACF1)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr23:5695113-5695733 
GgaINT0137882
(MACF1)
Zebrafish
(danRer10)
chr19:35492431-35495014 
LOW PSI
DreINT0091847
(macf1a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CCTCTCCTCCCTGACATGTCC

				
R: 
AGTTTGTTTTAGAAGAGCCTGACCA

				
Band lengths: 
343-1439

			

		

	





	
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"