Special

MmuINT0008019 @ mm9

Intron Retention

Gene
ENSMUSG00000035722 | Abca7
Description
ATP-binding cassette, sub-family A (ABC1), member 7 [Source:MGI Symbol;Acc:MGI:1351646]
Coordinates
chr10:79474020-79474587:+
Coord C1 exon
chr10:79474020-79474143
Coord A exon
chr10:79474144-79474457
Coord C2 exon
chr10:79474458-79474587
Length
314 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGA
5' ss Score
6.95
3' ss Seq
AGTTCTTCCTGTCCCCGTAGGAG
3' ss Score
10.62
Exon sequences
Seq C1 exon
AACCTGCAAGAAGTGAGCCGGATCCTGAAACAAGTGTTTCTTATTTTCCCCCACTTTTGCCTTGGCCGAGGGCTCATTGACATGGTTCGGAACCAGGCCATGGCAGATGCCTTTGAGCGCTTAG
Seq A exon
GTGAGACTGTCTGTCAGGTGGGGACTGTGAAGAGCATGATTGAGAGTGCCTCCTTCAAATTCAGTTATATGGAATGGGGACACATTGCCTTTAAGTGAACAATTTTAGGTGGCACAAAAATTGTGTCAAATTAAAGGTGAAGAAAATGTAACTAAAACGTTATATCATGAAAGCTCTGACTATACATAAAGGAGCATGTGAAACCTTATAGTCTAAGTCAGTTCTACCCTAGCAGTACAAGTCGTCTTGGTCACTTTTTTGAGTCTAGGGTGATCTGCACAGAGGGCAAGACCCAGTTCTTCCTGTCCCCGTAG
Seq C2 exon
GAGACAAGCAATTTCAGTCACCCCTACGCTGGGACATCATTGGCAAGAACCTCCTGGCCATGATGGCCCAGGGACCTCTGTTCCTCCTCATCACACTCCTGCTCCAACACCGCAACCGTCTCCTGCCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035722-Abca7:NM_013850:36
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF126982=ABC2_membrane_3=FE(12.1=100)

							
A:
NA

							
C2:
PF126982=ABC2_membrane_3=PD(9.8=75.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000128121





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000043090, ENSMUSP00000115111
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr19:1058270-1058617 
ALTERNATIVE
HsaINT0000812
(ABCA7)
Human
(hg19)
chr19:1058269-1058616 
ALTERNATIVE
HsaINT0000812
(ABCA7)
Rat
(rn6)
chr7:12746119-12746422 
LOW PSI
RnoINT0010380
(Abca7)
Cow
(bosTau6)
chr7:45177619-45177977 
ALTERNATIVE
BtaINT0011204
(ABCA7)
Chicken
(galGal4)
chr28:2825420-2825508 
LOW PSI
GgaINT0144870
(ABCA7)
Chicken
(galGal3)
chr8:14422961-14423628 
GgaINT0144870
(ABCA7)
Zebrafish
(danRer10)
chr1:51981178-51981591 
LOW PSI
DreINT0023534
(abca1a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AACCTGCAAGAAGTGAGCCG

				
R: 
TGTGGCAGGAGACGGTTGC

				
Band lengths: 
254-568

			

		

	





	
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"