Special

MmuINT0094317 @ mm9

Intron Retention

Gene
ENSMUSG00000028649 | Macf1
Description
microtubule-actin crosslinking factor 1 [Source:MGI Symbol;Acc:MGI:108559]
Coordinates
chr4:123189290-123190111:-
Coord C1 exon
chr4:123190005-123190111
Coord A exon
chr4:123189410-123190004
Coord C2 exon
chr4:123189290-123189409
Length
595 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAAA
5' ss Score
6.53
3' ss Seq
TGTTTGCCTTCTGACTGTAGGAA
3' ss Score
8.81
Exon sequences
Seq C1 exon
ATGTGGATGTGCCATCTCCAGATGAGAAGTCTGTAATCACTTACGTGTCTTCAATTTATGATGCCTTCCCCAAAGTCCCCGAGGGAGGAGAAGGGATCAGTGCTACG
Seq A exon
GTAAAAGGACATTTTCCTAAAATACCAAGTCACAGAGGTAGAAAGCCTCCATTAGATAGTGCTTTTTAGTTTCTTATGCATAGAGCACTTTCACAAAGACCACCTGACTCTACATTATCTCTGTCATAATGGACACTGTCCCTGAGAATGAGTCTGGGTATTGCTAATTTTGTGCCATCTAACATAGACCATTTGATGTTAAATGCCAGCCCCCCTCCCCAATGTTCTTTTTATTCCCAGCTGTAATTCAAGATGAAGCATTTTCATCTCAGCTACTGATAGAAGTTTGATTAGAGCCCCATTGTGCTCTAGGATAGCCTGCTGCCTCAGCCTCGCTGTGTTGTAATTACAGTGTGAAGAATCACCATGCTTGGAAAATACCCTACTTCATAATCAGAGTAGCTTGGTTTATAGTCTGTCTACCTGTCAGGATATTGAATGCCAGCTGGAGATTCCTTGGGGAGCTTTGAGATTGAGTCTCTGAGCACTCAAGAGAGAGTTTTATATGGTATGGGGTGACCTTGACTACTTTATCCTGTGCTGCTGCTGCTGCACAGTACAAATCGGATCTGTGATGTTTGCCTTCTGACTGTAG
Seq C2 exon
GAAGTGGACTCCAGATGGCAAGAATACCAAAGCCGAGTGGACTCACTCATTCCCTGGATCAGGCAGCATACGATCTTGATGTCAGATAAATCTTTTCCCCAGAACCCTGTTGAACTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028649-Macf1:NM_009600:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.056 A=NA C2=0.025
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0030726=CH=PD(22.5=63.9)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000081324f2416A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000080755, ENSMUSP00000081324, ENSMUSP00000081324f6186A, ENSMUSP00000095508, ENSMUSP00000095509, ENSMUSP00000101827, ENSMUSP00000101831, ENSMUSP00000101831f2417A, ENSMUSP00000114568, ENSMUSP00000115847, ENSMUSP00000123246
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:39283516-39284065 
ALTERNATIVE
HsaINT0098097
(MACF1)
Human
(hg19)
chr1:39749188-39749737 
ALTERNATIVE
HsaINT0098097
(MACF1)
Rat
(rn6)
chr5:141194099-141194677 
ALTERNATIVE
RnoINT0088199
(Macf1)
Cow
(bosTau6)
chr3:107336378-107336797 
LOW PSI
BtaINT0088436
(MACF1)
Chicken
(galGal4)
chr23:5326342-5326576 
LOW PSI
GgaINT0137833
([1])
Chicken
(galGal3)
chr23:5640985-5641219 
LOW PSI
GgaINT0137833
(MACF1)
Zebrafish
(danRer10)
chr19:35604508-35606237 
LOW PSI
DreINT0091866
(macf1a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGGATGTGCCATCTCCAGAT

				
R: 
TTAGTTCAACAGGGTTCTGGGG

				
Band lengths: 
222-817

			

		

	





	
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"