Special

MmuINT0008059 @ mm9

Intron Retention

Gene
ENSMUSG00000041828 | Abca8a
Description
ATP-binding cassette, sub-family A (ABC1), member 8a [Source:MGI Symbol;Acc:MGI:2386846]
Coordinates
chr11:109892874-109897896:-
Coord C1 exon
chr11:109897805-109897896
Coord A exon
chr11:109893035-109897804
Coord C2 exon
chr11:109892874-109893034
Length
4770 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
CAGTGACCTTCTCTCCATAGGTG
3' ss Score
10.75
Exon sequences
Seq C1 exon
GTGAGGTTGTAGGATTACTGGGACACAATGGAGCTGGTAAAAGTACATCCATTAAGATGATAACTGGAGAAACCAAGCCAAGCGCCGGACAG
Seq A exon
GTAGGTAGATGAGAGATAGTATTTTCTCCAATGATACCCAGATGACAACTTGAAAAACATTATCCTTCAAAGTTCTAAAAATATTATCCTGAATTATAAAGTGTCACTTTAAGTGGCGCAGGTACTAGCCGTTTGATGGGGATGCTTTTAAATGTTTTGATAATTTTATGGGTATGGAATTAATTTTATTATATTCAGCACCCTTTAGCTTTTCTCTTCTCCCTCTGTCTCACATTAAGACACTTTTTGTTCTCCAAAACCTTCCCTTCCACTTCGTGTACGACCCATTAAACTTCATTAGGGTGGCTTGCATGAGCGTGGGCATGAACAACTTATCAGTGGTTACATCACTGAGGAAAGTGATACTAGCTCCCTAGCTGCTATTAACGACCAGTAATCACCAGGGCCCCTGGGCTTCTCCACCATCCATCCCCGATGAGATGTTAGCAGGTCGTGGGTAGGTAACTGCAGCTGCTATCAATTCATGAATGCGAAGCACAGGTCATATTCAGGAGTTCACAGCTCTCCACCCCCATCCTATGCCTTTTATATTCTTTTTTGCTTCTTTGGTTTCAGTGTTCCCCAAGCCTTGGAAAGAGCAACAAAGATATTCGATTTAGTTCTGAGCACTTAAGAATCACTTAATGTCTGTACCACTTATGAATATTATCCCATTGCAATAGGAACCTTCTTTGACCACGACTGAGAATAGCTCTGATCTTTAACTGTAAACATAAACGCTTAGCAGGCATCTGGGAATGCTTTGAAACTATCCTTTTCCCATGAGTGTATTAAGAAGGAATGTTATTCATCTTTGGAATACTAATTATTATAAAAAACCTTGACAGACTCTGTTTATTGGACCACATAATCCACTAATTATAATTTTAAATGGCTTTTATAATTAATTTCAGCCTGCTATTGCTCATCTTCCTGAAGTACCATTTGTAACTCATAAATCTTTCACAGTCATACAAAAACCTTTCTTGTACGAATCCAATAAGGTGCTTCTTAAAGTAGCAGAGCGTGGAGAAGCATTCATGTAAAGCCGAACTGCTTGCCAGCTTGTCACTTGTTTCAGAAGCAAAATGGCCAGGCAAACAAAGTTCAGACTTAGCCATGAGAGCCGATCCCAGGGAAGAGGCAGGTCATTCCCTTTTCTCCCTTTACAGGGCAGAACTGCTTTAGAAAGTGACTAGGGGAAGGGCAGATGTCTGTGTAACTATGCCAGAAGAGAATGTTGGTAATCAAACTAGAGAGGGAGAAGAGAGGCAGGGATATAACTGTCATACATCCCACTATGTAGGGAGGAGAAACTCACGTGCACAGTCCCTCTGAAGCCATGGTGGAGCAGAAAGCCAGAAGCAGGTCTCTGCAATGTTCATGGCACAGCCTACCTTAGCAGGACTCCTCAACTCCAGCTACAAATGCCATTCCTCGCCACACACCACCTAGCTTTAACTACTTCAATGGCTTGCCTGCTCTGGGACTGGCATGCCAGCTCTGGCTTGTCTTGCAGGTAGCTTCAAGAGTTGCCTTTTATATCTGTTCTCAACCTCTGTCCCTGGGCCCTTCTTCACTCTACACAAATCTACTTCTGATCTCTGAGATTGGCCAAGGATACATCAAACTTCATCCTTCTACAGCCCTTTGCTCCTGGTCTTTGATCTTGTACAAATGTGTTTCTCCTAGCCCTGTCCACAGCTAATACCTCCTTCTCCTCTCCTGACATGGCAGTTCAGCAGGATAATGATCTGAATGAGGTAAAAACCCAGTTCAATACAATTTCGCTGGTCTTGTCTCAAAAGTCTAGATTCTGATCATGAATAGTTTATCTTTGTCATATTTAAGAAAAGTACAACTTTGAGAAAAAGTTTTTTCATAACAATTACATAATAAATACTAAGGCTGGTCTATATAAAAAATAAAATTGTCATGTTAGGCAATTATAGTAAGCAATTTTATTATAATGTAAATTATCATTACAATTTATTCTATAGTAAGGTATTTTATTAATGTAAAAATGTTTTGAGACCTCAGCCATAATGTTAAGATGCAAAATGTCTGGCATAGTTCATTTCTCTTTTTGCTTTAAAAACATGATTAGCTAGGGAGAAAACCTGGCCCATCTCCGGGACTTGTTGGCCAGCTTGCCTTGCCTACTTGGTGAGTTCCAGACAAGGAGAGCCCTGTCTCCAAAACCAAAGTAGGGTCTGAGGAGATAGCTCAGTTAGCAAAGGGCGTGTCTAGCGTGAGGTAGAGGTCATGTGACACTCCCAGTGCTGCTTCTATCTTCACACCCACTGTGGCATGCGTGTTCCCACACTCACACACTCTCAAACAATCAAACATGTACGCTAAACCTAAAATACTAATTGATCTTTTAAAAGCTTCCAAATGGCATTACAATTGGACATCTTCATGAGGTACAAAGCAGATCTTTGGATGAGCCTCCAACGTGGAATGATTAAATGAAGTCACTTTTGTGCATGCTCCTTGCAGCCACTATTCTGTGCCGTCAATGCTAGAGCTCCCTCGGCCTTCTAAATGAGACTGCTGGTTTGGATCAATCCCTCTCTTCCTTTTCCAATCTCCACGGCTCATCATTCTTCTTGTTTATACTTTTGATTGTGAGCCTCCCCTTTAAGGGCTGAGCCTGTGAGCCTCCCCTTTAAGAGCTGAGCTATTGCTTCAAGTTTAACTCATTTAAATGGTGTGTGTGCATATTAATGAAGTCAGGCAGTGTCTGTCTTCTGTGCCCACTTTATTTTGCATCCCACAATTATCATGGTTAGTCAACCTGACACAGACCTAGACATAGTGAAGAAGAGGGACTCTTAACCAAGGAGTTGACACCATCAGATTGCACTAAGGGCACATCTGTGGGGCATCTTCTTGATTGCTAACTGATGTGGAGAGACTCAGACCACCATGGGAAGTACCACATTTGGGCAGATGGGTCTGGGCTATATAAGAAATGTAATGAGCAAAGTGAGGGAAACCTAAGCCAGTAAGCAGCATCCCTCCATGGTTTTTCCTTCAGTTCCTGCTTTTGTGTTCCTATACTGAGTCCCTGCCTTGACTTCTGTCGAGAATGGACCATGATCTGGAAGTGGAGGCCTAAATAAACCCTTTCCTCCTCAAGTTGCCTTTGGTCAGAGTTTTATCACAGCCATAGAAAGCAAAGCATCTCATATTTCCTAGGTCCATCCATGTTACCACAGACAAAAGGAGACCTTCCATCTTAAAGGCTGAATAATATCAAGTTGTGTCTGTATCACCGCATTTGAAAACCCATTAACCCTGAAATGGACATTTGGTTGACTTCATCTTCTCTACTGCAAATAGGAACACAATACTGAAAACAGTGATTGGTTGATAAGGCAAAGCAAAGAAGAAAAGAAAAGGAACTTTCAATCCCTTTGAAAACATTCCAGGAAATGAGCCATGTCCTCCCCATTCCCCACACTTCCAGGTCATACCTCAGCCATGCCCTCCCCATCCCCCACAGCTCCAGGTCATACCTCAGCCATGTCCACCCCATCCCCCACACTTCCAGGTCATACCCCAGCCATGTCCACCCCATCCCCCACAGCTCCAGGTCATACCTCAGCCATGTCCACCCCATCCCCCACACTTCCAGGTCATACCTCAGCCATGTCCACCCCATCCCCCACAGCTCCAGGTCATACCTCAGCCATGTCCACCCCATCCCCCACAGCTCCAGGTCATACCTCAGCCATGCCCTCCCCATCCCCCACAGCTCCAGGTCATACCTCAGCCATGTCCACCCCATCCCCCACAGCTCCAGGTCATACCTCAGCCATGCCCTCCCCATCCCCCACACTTCCAGGTCATACCTCAGCCATGTCCACCCCATCCCCCACAGATCCAGGTCATACCTCAGCCATGTCCACCCCATCCCCCACAGCTCCAGGTCATACCTCAGCCATGCCCTCCCCATCCCCCACAGCTCCAGGTCATACCTCAGCCATGCCCTCCCCATCCCCCACAGCTCCAGGTCATACCTCAGCCATGCCCTCCCCATCTCCCACAGCTCCAGGTCATACCTCAGCCATGCCCTGTTCCCCCATGCCCCGCAGGGGACATGGTGCAGTTTTTCCATAACTGACTATACTAATTCGTACTTGCACCAACTAAGGACAACAGCTCCATCTTCTCCACCTCCTTATCATTTCTTCTCCACTTTCCTCCCTTTTGATAGCAGCCCCTTTACTGATGTGAAGTGATATCACACCATTTATTTGTATGTACATATTCATATGTGTGCATGTGTGAGCATGCGTGTAGAGCCAAGAAGTTAATGTTGGATGTCTTCCTCAGTAACCCCCCCCTTTTTTTTTTAATCTGAGACTGTCTTTCAGTGAATCTGGGTTTACTCATTTGCATTGATTGGCTGGTTATCAAGTTCCTGGGGCTCTTTCTGTCACTGTCTACCCAGCTTTGGGTTCTAGGTGTAACACTGCTGTAACTGTAATGTGGACGCTGGGATTGGATTCAGGTCCTTGTGCTTATGCGGCAAGCACTTTAGCCATTTCTCCAGCCCCTTGCCATGGTTTTTATTAACATTTTCCTGTAGATCATCCTTTAATATAAGGTAATGTGGCACCTTTGCACACACTTGAGTCCATGCATTTGTTCTCTGGATGAATCCTTCCGCCTTTCTGAGATGATCACTGAAGTCTGCCACAGAAGCACTTTGGGGAACAGTACCGAGTTTGATCCCTGACAGTGACCTTCTCTCCATAG
Seq C2 exon
GTGCTGCTGAAGGGGAGCAGCACAGGGGACACCCCGGGGTTCCTGGGGTACTGTCCTCAGGAAAATGCTCTGTGGCTCAACCTGACAGTGAGGGAACACCTGGAGATATTTGCAGCCATAAAGGGGATGAGAAAAAGTGACGCGAACGTGGCCATCGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041828-Abca8a:NM_153145:31
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.161 A=NA C2=0.056
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0000522=ABC_tran=FE(21.3=100)

							
A:
NA

							
C2:
PF0000522=ABC_tran=FE(37.6=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)
chr17:69154010-69154234 
ALTERNATIVE
HsaINT0000436
(ABCA10)
Human
(hg19)
chr17:67150151-67150375 
ALTERNATIVE
HsaINT0000436
(ABCA10)
Rat
(rn6)
chr10:98326067-98330351 
LOW PSI
RnoINT0010459
(Abca8a)
Cow
(bosTau6)
chr19:62143603-62147309 
ALTERNATIVE
BtaINT0011244
(ABCA9)
Chicken
(galGal4)
chr18:8235811-8235966 
ALTERNATIVE
GgaINT0127860
(ABCA5)
Chicken
(galGal3)
chr18:7945839-7946533 
ALTERNATIVE
GgaINT0127079
([1])
Zebrafish
(danRer10)
chr12:38674902-38674985 
LOW PSI
DreINT0023737
(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"