Special

MmuINT0008045 @ mm9

Intron Retention

Gene
ENSMUSG00000041828 | Abca8a
Description
ATP-binding cassette, sub-family A (ABC1), member 8a [Source:MGI Symbol;Acc:MGI:2386846]
Coordinates
chr11:109921194-109924534:-
Coord C1 exon
chr11:109924336-109924534
Coord A exon
chr11:109921361-109924335
Coord C2 exon
chr11:109921194-109921360
Length
2975 bp
Sequences
Splice sites
5' ss Seq
TCTGTGAGT
5' ss Score
7
3' ss Seq
CAATTATTTTTTCTGTTTAGGAT
3' ss Score
9.7
Exon sequences
Seq C1 exon
ATATTGGTATGACAGAAGATGTACAAGCTGGAGGGGCAAGGAGCCCAGAGAGGTTTGCTGAAGTAGAACAACTTGTCTCTTTACTTAATGGGAGGTGTAAGATGAAGGGGGGCATGGCTCTATGGTGGCAGCAACTCTGTGCAGTGACCAGGCTTCGCTTCTTGAAGTTAAAGCATGAAAGGAAATCCATCGTTATTCT
Seq A exon
GTGAGTACTAAATTATCGTTGCAGATTCCAATTGTTGCATTAAAGCACACATAAGTAAAACGATAAAAATAAATCCCAGAGCAGGTCCCTACTTGCTATTTCTGTTAATAGTCTTGGTATTCACACATTATTATAGTAACACATAGAATGAAAAAAAAAAATCTCTCAGAGATAGTATGAGGCCTGGGGTCTTTCTTCATTACCATCTCTCCTTTAAAGTCTCCACAGTAGAAACAATGAACACCTTAGAACTTAGCCTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATCTCCTGATTCAGATTTCACAGAATTCTCTGGGACTGTAATGGGTTTGTAAAGTTGATACATCTTCAAATTCTCTCTCTTTTCTGTGGTTCTTATGTGCAATTGGTCCCTTATCAATTCCTGCCAGATGTCAGGCATTTTTAGGAGTTGGACATAAAAGATACCAATTGTCTCTCAAGGAATTTATCTCTTGACATTATCGCCCTGAGATCATCTCATGGTCAATCAATAAGTTGTAAATCAGTTCACATAGAGGAGCCAGGACTTATACTAGAATCCCAGTCAATACTTGCTGAATACATGCTTCAAATGGAGGACATTATCAAGATTAAGACTAGAAGAAAACTATTTGTAGTTAATTCAGAAATGCTTTGTAATACAAACTGGGAGGTGCAAGAACAGAGGGATGCCAGCCACAGAGCCCAGCAGGCAAGAAGTCTTGGAGTTCCTCATGTGCTGGGGCCCTTTCCCAGCCTGTTGACAGGATGGCCCCTAAGAGGAGATGAGGAGTCAGGTGTGACTCAGATAAGGGATGAGTGAGTCAGGTGTGGTGGTCAGAGGAATCTTGCAGCTCGGACTGACTAGCAATCAGGTCACCTTTTTACTTATACCGTTCATAGAACAAAGACAGACTAATGCTTATCCAAGAAGTCCACAGTATATCCTTTTATCTATGGACATGTGTTTGATTTTCCATTACAAATCTGGGGTTACAAGTTCAGTCACAATTAGAAAGCACAAATAGAACAGATTTTATTTTTATTATTAGCCCTATCACTCCAATTCAAAGATTCTGAAGAATGTTTCTGTCAAAGCAAACACATTTATTATATAACAACAGCCTGATTTTAGGCTGGCAGTATTTACAGTTTTAAAGCACCTCAAACAAGCAGAAAATACCTAAACTGGTCTTTTTTATGAATAGCAAATACTAATACCTATCTCCCTTTACAATATTATTTCATCATCTATGTTATAAGACAGAAAATGTTTATTTTGGTCAATCTTCCTAATTTAGTGGGGTCTAGTCTTTCAGGGGTGTTCCTTGTATGATTCCCTATCTCTAAACTAAAATTTCAGAGAGATCTAAGCATATTATAAAAGGGAGCCTAGACTCTGTTGCTAATTATCCTAGTCAGTAAGGGTTTACCTTTTACCAATTATACTGTTTGAGCTTGCTTAAGGGCAGATACCCGAAGAGGATTCCTGGGCTTGTGGTCTCCTTTACAACTTCCTAGCTTTTGTTTATCCTAGCTTATTGCAATCTCTAGGGCACAAGGAAGTTTTCCAAATAGAGGCCAGATAAAGCAGAGGTGAGTTTAGGACTTTCCTTAAAAAAGACTCAGAAATCATTTTCTCAGGAAAAGACATACAATGAGTCATAATGCAGAGTTTCCACAAATGTAACACACAGAGACAAGAACCCAGAAGTGAGAGACAGAAGGACAGCCATCACAGCATTCAGCCCAGCTTTGCTGGAACTGTGTCAAACAGCTGTGCTGACTTCACAACGTTTGCGTTTCCCAGTGGCTGTGGCCGTGCCACCCATGCTTGGAAGGAAATAAGGATGAGGTTTCCGCATTAGTGCTGAAGTGCTGGGATCCAAGTTTTAAACTTTTCAAATGGGAATCAAAGGAAAGGAAAACACAAAAATAAGTAATGGCTTATGTCAGTGAGGCTTAAGAAACTGTTACTATGTCCAATTTTCTGATGAACCGCCAGACTGACTTCCAGAGTGGTTGTACAAGCTTGCAATCCCACCAGCAATGGAGGCGTGTTCCTCTTTCTCCACATCCTCACCAGCATCTGCTGTCACCTGAATTTTTGATCTTAGCCATTCTGACTGGTGTGAGATGGAATCTCAGGGCTGTTTTGATTTGCATTTCCCTGATGATTAAGGATGTTGAACATTTTTTCAAGTGCTTCTCAGCCATTCAGTATTCCTCAGGTGAGAATTCTTTGTTTAGCTCTGTACTCCATTTTTTAATGGGCTTATTTGGATTTCTGGAGTTCAGCTTCTTGAGCTCTTTGTATATATTGGATATTAGTCCCCTATCAGATTTAGGATTGGTAAAAAAAATCCTTTCCCAATCTGTTGGTGGCCTTTTTGTCTTATTGACAGTGTCTTTTGCCTTACAGAAGCTTTGCAATTTTATGAGGTCCCATTTGTCAGTTCTTGATCTTACAGCACAAGCCATGGAAGGGGGAGGGTATAGGGAATTTTTGGGATAGTATTTGAAATGTAAATAAAGAAAATACCTAATTAAAAAAAAAAAGAAAAAGAAACTGTTACCATGAGCAAAACTAGAGACAATGGTTAGGAGAGCAGAGAGCAAAGAGCAAAGAGCAACTCGTGAGTCTGGGGAGTGGTGCACTGTGCAGCAGAGAGGGAACAGTAGGATAAACACAGAGAAAACAAGGCTAGAGCTCAACTTGCCATGTAAGGACATTGCACAAGCTGTCCCATGATCAGAGGGCATCAAGCGAAGTGTGCTGATGGGGAATCCTTGGTTTTTGCTCCCACTTTAAAGACAAGGAATAATTTAAGAACCAAGACAAAGGACCACACATATGAATGTCTGTCTCTAATAATGCCTTGCTTGTAGTATATCCATGCCTTTGAAAGAATGCTCTGAAGACTGGACAATGGCTAGAGCTCTACGCTGTCAATTATTTTTTCTGTTTAG
Seq C2 exon
GATTCTGGTTTTGGGGATTGGACTTCTGCATATTTTGTCAGCAAATATTTACAGGATGGTCCGTCAAAGTGACTACTGTTGGGAGCTTGCCCCTCATATGTACTTCCTCACACCAGGCCAGCAACCACAGCCGCCCCTCACGAACTTACTGATCGTCAACAAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041828-Abca8a:NM_153145:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.015 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF126982=ABC2_membrane_3=PU(0.8=4.5)

							
A:
NA

							
C2:
PF126982=ABC2_membrane_3=FE(15.8=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000097860





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000045808, ENSMUSP00000102275
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr17:69185644-69187680 
ALTERNATIVE
HsaINT0000423
(ABCA10)
Human
(hg19)
chr17:67181785-67183821 
ALTERNATIVE
HsaINT0000423
(ABCA10)
Rat
(rn6)
chr10:98604818-98606382 
LOW PSI
RnoINT0010284
(Abca5)
Cow
(bosTau6)
chr19:62126687-62129196 
LOW PSI
BtaINT0011230
(ABCA9)
Chicken
(galGal4)
chr18:8241696-8241920 
ALTERNATIVE
GgaINT0127848
(ABCA5)
Chicken
(galGal3)
chr18:7977187-7977411 
LOW PSI
GgaINT0127848
(E1BY40_CHICK)
Zebrafish
(danRer10)
chr12:38665595-38667313 
LOW PSI
DreINT0023723
(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"