Special

MmuINT0007950 @ mm9

Intron Retention

Gene
ENSMUSG00000018800 | Abca5
Description
ATP-binding cassette, sub-family A (ABC1), member 5 [Source:MGI Symbol;Acc:MGI:2386607]
Coordinates
chr11:110175838-110179245:-
Coord C1 exon
chr11:110179016-110179245
Coord A exon
chr11:110175980-110179015
Coord C2 exon
chr11:110175838-110175979
Length
3036 bp
Sequences
Splice sites
5' ss Seq
TTGGTATGT
5' ss Score
7.12
3' ss Seq
TGTTTGCACTTCCATCGTAGGCT
3' ss Score
7.65
Exon sequences
Seq C1 exon
CTGAAGACCAATGTTTCTGTGTGGAGCGAGCTGGAGTCGACCAAAGCTGTGATCATGGGAGAGGCCGCTGTTGTGGAGATTGACACCTTCCCGCGAGGGGTCATCCTCATCTACCTCGTCATAGCCTTCTCGCCCTTCGGCTACTTCCTGGCAATCCACATCGTGGCAGAAAAAGAAAAGAAGTTAAAGGAATTTTTAAAGATAATGGGACTTCATGACACTGCTTTTTG
Seq A exon
GTATGTTTCGTGGCTTCCGGTTTGGTATAGTTAACAGCTGTATTGACTCTAGTGATCTTCAGCAGTCTCCTTTTACTTCCCAGTCTGCTGTGCTGTGCTGTGCTGGTCCTTCTAATGGCTCCACTTTTCTTAGACTTTGAGACTAGTCAATTAGCTGCTTGTTTTATTGGAAGTTGCTGTTGACAGTGTATTTTATTTTACAACCTGTTCGAACCCTTGAGTCACGCATCATGTATATCATTGCATCACTGCACGGAAGATAGGAAATCTCTAAAAACTCGAAGTTGCCTACTAATGCCCTTTCCTGATATCAGAGCAGATACTCAACACTGAAAGCTTAGTTCACAGATGAAGGTCTACTCATGTAGCTTCTAGCTTCTGCTCACTTGGAGCTTCAGTAAGTTACGATAAGGATGTGTAGGTAATTTATGGAGACACAAGTGAAGAAAAAAGTTCCCATAGTTAAGAGGTAAAATATTAGCATTTTTATACAGTGCTAATTTTTTTTCATAATTTATTTCTATTCACATTATATCTCAATCAGTCACAGTCTCCCACCCTCCTCTCTTCCCATTCCTGCTCTTACAACCCCCTGTCCCTATTACTGCTTCCCCTTCTCCTCATAGAAGGAAGCCACTCTTGGGTACTGTTCCACCCTGGGACATCTCGTCCCAGCAGGACTAAGCACCTCTTTTCCCAAGGAGGCCCAACCAGGAAGCCCAGTTAGGTGAAAGAGATCCAGTGGCAGGCAACAGAGAGAGTCAGAGTCAGCTCCCACTCCAACTGTTAGGGGATCCACAGGAAGACCAAGCTGCATATCTGCTACAAATGTTGGGAGTGGGAGCTAGGTCCAGCCCCTGCATGCTCTTTGGTTGGTGGTCCAGCCTCTGTGAGCCCCCATGGGGTCAGGAGAGTTGACTCTGTAGGTCTTCTTGTGGTGTCCTTGACCCACAAAATACTGCTTAAATATTTTAAATGAACCTTTAAAAGAGAACTACCTTTTGTGAGACTTGCAGTTAACAAAAACAAACAAACAAACAAACAACAACAACAACAACAACAAAACAAACAGAAAATGGAAGCTCCTGCTGGAGGCTGGAGTTAGAAAGGCCTTTTTGTATTCACCAGAGACAGAGGAGGCAACTGGTGAGCACAGCTGAGAACAGGGTCAGCAAGATGGAACACAGACCAATTGCTCTGCAGTGCTAATTTTATAGAGACATGGATAGTTATAAATAAGTACTTTCCTCTCCTATTTCTTCTGTGTAATAAGACAATTTGTTTGTAAGCTGGCTGGCTTGTGCCTGCCTATAATGCTAGCACTCGGGAATCAAGTCAGGAGGGCCTTGAGTCTGAGGCCAACCTACGCTAGATTGCCAGACGCTGTCTCAAACAAAAATTGGTTTCTTTTTAGCCTATTTAAGAGGAAGGTTAGTACTTTTAATGGAAACTGTTAAGTTTATGGTTTTTATTATTGCATTTACAAAACAATTTTGTATTTTACAATTTTTTTTGTTTTGTTTTTTTGTTTTTTGAGACAGGGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAAGCAGGCGAAATCCGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGCGCCACCACACCCGGCTGCATTTTACAATTTTTAAAAAAGATTTATTTTATTTATATGAGTAAACTGTAGGTATCTTCAGACACACCAGAAGAAGGCATAAGGTCCCATTACAGATGGTCATGAGCCACCATGTGGTTGCTGGGAATTGAACTTAGGACCTCTGGAAGATCAGTCACTGCTCTTAACTGCTGAGCCATCTCTCCAGCCCTCATTTTACAAATTTTTATTTGGTCTGTTGTAACATGTATAAAACTTGATGTAGTTAGTGGTATTATTATGTCTTCACATTTTCTCTGCTTTTTAAATTATTATTTCACATGTATGGATGCTTTGCCTGCATGCCTGCATATGCACTATGTTTATACAGTGTCTGCAGAAGCCACAAGAGGCGTTTGGATTCCCTGGAACTGGAGTTAGAGAGAGTTCTTAGCCATCACACTGGTCCTAGGAATCAAACCCAGGTCATCTGCAAGAGCAACAGTGGTCTTAACCACTGAGCCATCTCTCCAACCCCCCACCCCCACCCCCCCACCCCCGCCTTTTTTGAGAGAGGGTCTCCTCATGTAACTCTGTCTTGGAGCTTCCTAGGTGAATCAGGCTGGCCTTGAACTCACAGGAACTTGCCTTCTTCTGCCTCCTGAGTGCTGGGATTAAAGGTGTGCATCAGTACACCCACCTTTTGTTTTTCTTAAATGTTCTAGAAATGGCCTTTAAGATGCATTGTATTATTATTTTTGTATTGAAATTGCTAGATAAATTTAGCTCTAAGTACTTAATATGTATCAACTCAATTAAATATTTTAAATAAATTTGAAGTTTTCTTTAAAATGGTTTTTCAATGCTAATGGGAAAATAAATAAAATGTGAAATTAAATACTAATGGTAATTCCACTGAGCTCTGACTGAAGGGAAAAGTTGAATTGAAATAGTGATTCTAGTTGATCTTATTAATCAGTACTCACATTGTATAAGTATGGTAATTATTGCTATTAATTGGTAAGGACATTTGGGTTTATGATAACCAAAGCCATCAGGGGTATAAGCATAGTTCATTTCATAAAGAAAATAATTGTATTGAATTAGCAAACACTTACATTTTAAGAGAATCAGAGATGCCAGTGCTCTCAGGCTTTTGAGAGTTTGAGCTTTAAATTTAGCATGCATTGCTATTGAATTGTAAAGCTTTTGACTCAGAGATCATTTTATCTCTGTCAGTCACATCCACCTGCAGCTTGGCTAGTCCTTTATTCTCCATTTCCTAATATTAGTGTTGGGTGCATGAACACACGCAGATAAATTGATTTGAAGAGTAAAATGGCGTTTAGTGTAAAGTGGTTTGTTCACTCCCGGAGCCTGTTCATTTGACAGCAGTGTGTTTGCACTTCCATCGTAG
Seq C2 exon
GCTTTCCTGGGTTCTTCTGTACGCAAGCTTGATTTTCCTTATGTCCCTGCTTATGGCTGTCATCGCAACAGCTTCTTCGTTATTCCCTCAGAGTAGCAGCATTGTGATCTTTCTACTGTTCTTCTTATATGGATTGTCATCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000018800-Abca5:NM_147219:6
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(19.6=100)

							
A:
NA

							
C2:
PF126982=ABC2_membrane_3=FE(12.1=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000047927





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000120708
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr17:69304811-69306724 
LOW PSI
HsaINT1000132
(ABCA5)
Human
(hg19)
chr17:67300952-67302865 
HsaINT0000739
(ABCA5)
Rat
(rn6)
chr10:98621984-98624365 
LOW PSI
RnoINT0010309
(Abca5)
Cow
(bosTau6)
chr19:61878668-61880428 
LOW PSI
BtaINT0011134
(ABCA5)
Chicken
(galGal4)
chr18:8249754-8250679 
ALTERNATIVE
GgaINT0127835
(ABCA5)
Chicken
(galGal3)
chr18:7985245-7986170 
LOW PSI
GgaINT0127835
(E1BY40_CHICK)
Zebrafish
(danRer10)
chr12:38648501-38648589 
LOW PSI
DreINT0023747
(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"