Special

MmuINT0008147 @ mm9

Intron Retention

Gene
ENSMUSG00000041797 | Abca9
Description
ATP-binding cassette, sub-family A (ABC1), member 9 [Source:MGI Symbol;Acc:MGI:2386796]
Coordinates
chr11:110013260-110015877:-
Coord C1 exon
chr11:110015692-110015877
Coord A exon
chr11:110013408-110015691
Coord C2 exon
chr11:110013260-110013407
Length
2284 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TTTATGCATCTCTTTTTCAGCTT
3' ss Score
9.3
Exon sequences
Seq C1 exon
ATAACTTTATCTTTCCTCATGAGTGTGTTGATAAAGAAACCGTTTCTTACTGGCTTGGCTATCTTCATCCTTACCGTCTTCTGGGGAAGTCTGGGATTCACAGCGTTATACAAACATCTTCCTGCCTTTGTGGAATGGACCTTGTGTTTTCTTAGCCCCTTTGCCTTTACCACTGGAATGGCCCAG
Seq A exon
GTAAGAAGGGAGGCAATTGTTTTGCTTTATTTTATTAAAACTTGTCTGTCTGTCTACATGTGTGTAAGTGCACATGCAAAGGCATGTCATAACGATGTTTGCATGGAGGTCAGGGGACAATGTGACAGATATCAGTTCTCTCCTTCCACCATGTTGGTTGTGGGGATCAAACCCAGGCGCTTTTACCTGCTGAGTTGTCTTTGCTGTCCTACAATTTTACCTTTGTACACAACACTCAAGATAGTTTCCTTCAATGACTTATACAGTGTATCCCAAACATCAACATTTCTCTCCCATGTTTGGAAAAAAACAAGTTTAAGGGATAGAGAAGTTTAAGATATAAGAGACATATTTATTTTTCTCTCCCAGCATATTTGTTTTCTCTTATATTAAATTTTGTTTTATTTATTTTCACTTTTGTTCTTTTTCAAGATAGGGTTTCCAAGTGCAGCCCTGGCTGTCCTGGAACTAGCTCTGTAGACCAGGCTGCCCTTGCACTCACAGAGATCAGCATGTCTTTCCCTCCTGAGTGTTGGGATTAGCCACCATTACCCAGCTAAACTTTTAAAAAATGTATAACCACATCATAGTCTCCCTTCCCTTTCCTCCTCCTCCACCCCTTCCATAGCTTTCCTTTATATCTACACCACCCCCTTTCAAATTCATGTCCTGTTTTTCTTCAATTGTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATCTCTCTCACCACTCAATTACCAAGTAGGAGCTCATCCTTTGGAAAGACTAATTACTTGTCTAGCATCATCCTTAGTTGCCTGTAGTTCTTTGGTGGTGGTGGGGCCATGTGAGATTTCCCTTTCTCCCATCAGTGTGTCTATCAGTGTCCTTTTCAGGTTTTATTCAGGCACATTGTTCAGCTATGATGAGTTATTTCTCAGAGACAGTCTCCTGGTAGTTTTCCATTCCTCTGGCTCTTAACATCTTTCTTCTGTTTCCTGAACCCAGCACAGAGATTGTGCCGTAAGTGTATCCATTTCAGTTGAGTTCAGCTGAGAACCCTGCTCACAATCAGTTGTTCTTTACATTTTGACCAATTGGAGATTTCTATAGTGGTCTCCATTTTCATAAAGCAAAGTGTCTTTGATGAGAATCGAGAGCTGTGCTTAGTTGTGGCAATAAGGATGAGTCTTTAGAATGTAGTTGGAAACTGTGCTGATTTAGAGAAGTGGCAACAGATCTTCTAAGATCCTTGGCCTCACAAGCCCTGGGTAGTTGGCCAGATTGCCTGTACCAGACATGAATTCCCTCTTATGGAGTAAGGCTTCAGTTGGGTTAGAGAGCTGTTGGTTACTGACAAGATGTGGGTGCCACACTTGCACAGTTAGGGTTCTTTTGTGTTTGGTAGGCATCACAACTGCACAGGACTCTAAGTTGCTTCCCTCACTTGGCAGCTTGCACCACTGTCCCATACTCTGAAAACTAGTCCTTAAGGAGGTAGCTTTTAAGTCAGATCTAGGTCAAATCCTGAGTTCCAAGCATGACATTTTTAGCAATAAGGATTTACTTTCAACCTCTGGGAGACAATAGCAATAGCCTGTATTGTTTGGGGAGTCTCTTGGACTCCCATAAACAATAACTTGAGGTTGGCTTCTCATGGGTTGAACTGCGATTTTTGTTAGACTCTGGCTCTAAATGGAGGATGACATTTGCTTTTTGATATGGCCCAGCTTATACTTCTAACTGAATACTTCTCAGATTTAAGCTTGAGAAACATGTGCCTTTAATGGTATCTATCACAAGTGTTGGAAAATCGAGACTTTGGAAAAGAATTGGACATTTCCACATGAAATTAAATCTCCCCTCAGAAAAGTTAATTCATGTGAAATCATTGTATCTTGGTTAGAATTATTCTTCTCTTTCTGCTCAGCTTCTAAGAAACTTTCATTTCTCCATTTTTCACTCTGAAATGTAATTTTAAAAATTATAATTATAAAATTATAATAGAATGCCTCGAGAACACCTCCCCATTCATACCTTTCAATCCTGATGGATTTGTGCTTTAGATGTGTCTCAAATACTACCTTTCTGGAGTTTTGATCTCTTCTAAGGAGATTTACCTACCACCTGCAGTTTGTAATTAGATGAGCAGTGGCCATGAACAGCAATAGGCCTGATACAGAGATATAAATTGTGTCTCATTCATCTCTCCCTTGGTTTCTAGCAGAACCAAGACCATAATTATCCTTAAAACTACACTAATCCCTTAAAATTTTATGCATCTCTTTTTCAG
Seq C2 exon
CTTATACATTTGGACTATGATGTGAATTCTAATGTAAATTTGAACTCTCCAAACAACTCGTACCTAATCATGGCCACGCTCTTCATGCTGGTTTTGGATGCTCTTCTCTATTTGGTACTGGCGTTATATTTTGACAAAATTACACTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041797-Abca9:NM_147220:8
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(15.6=100)

							
A:
NA

							
C2:
PF126982=ABC2_membrane_3=PD(10.7=84.0)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000115422





     
                   









    
Main Skipping Isoform:
ENSMUSP00000036338





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr17:69033874-69035245 
ALTERNATIVE
HsaINT0000901
(ABCA9)
Human
(hg19)
chr17:67030015-67031386 
LOW PSI
HsaINT0000901
(ABCA9)
Rat
(rn6)
chr10:98458276-98460599 
LOW PSI
RnoINT0010509
(Abca9)
Cow
(bosTau6)
chr19:62111596-62113102 
LOW PSI
BtaINT0011254
(ABCA9)
Chicken
(galGal4)
chr18:8199525-8199667 
ALTERNATIVE
GgaINT0129138
([1])
Chicken
(galGal3)
chr18:7958108-7958676 
LOW PSI
GgaINT0127456
([2])
Zebrafish
(danRer10)
chr12:38651525-38652929 
LOW PSI
DreINT0023749
(abca5)
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"