Special

MmuINT0007918 @ mm9

Intron Retention

Gene
ENSMUSG00000018800 | Abca5
Description
ATP-binding cassette, sub-family A (ABC1), member 5 [Source:MGI Symbol;Acc:MGI:2386607]
Coordinates
chr11:110167559-110170762:-
Coord C1 exon
chr11:110170704-110170762
Coord A exon
chr11:110167670-110170703
Coord C2 exon
chr11:110167559-110167669
Length
3034 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGT
5' ss Score
9.82
3' ss Seq
TATTTTTTTCCATGAACTAGATT
3' ss Score
4.63
Exon sequences
Seq C1 exon
AATAAGTGGTATTCAGAAATCCTATAGAAAGAAAACTGAGAACGTGGAGGCTTTGAGAA
Seq A exon
GTAAGTGGCTGGCCGAGGACTTAGTCCATAGCATCGTAGTACAGACAGAGAACCAGTCTGCATCGTTGTTGTGAAAGTTAAATTTACCTGTTAAGATTTGCTGTCTTCCCATTAGAGACACTTTAGGTGACTAATGTAGATAATAAAACTTACGACATGGAAGCTATAAAGCCAGAAAGTAGTATCTGTTGACGTGAAAATACCTATCAATTGCTGGAGACTCCGTAAAGAAGTTATTATCCCTGCGCATACTGGGAGCCTTTGCTTCCTAAACCAACACTCTTCTGCACAAAGGATAAAGGAATGGATGTGCTGCCAAAAAAAAAAAAAAAAAAAAGAAAGAAAAAAAAAAGAAAAGAAAAGAAGAAAAGAGAAAATACCTAACAATTTGAACCAGTTTATATTATATTCTGGTTCAATGAATATTATATTTTATTATTGTGTACATGTATAGGCATTACTTATATAGTTGTAAGATTCTTTTTGTGTGTGTGTGAAGTCTGTCTGGAGAATTGGAGTACATCTAGCAATGTGTCAGTATCTCCCAGGATCTGTAAAATACACTTACACACTGACATTTGTCATTCGAGAGACTGTATTCTGGTAGGGCCCAGTAGTGTGTCAGTATGCTTCTATCTTACGTTGGCCCAGGGTATAATGCATCTTGTTATCCCTTCGTTGGACATTCGAATGTTCTTTTTAAATAGTACCTACTTAAGGTTTACTTAAGTTAAGTATTAAATATTTTTAATATTTTAGGTTCATGGCCTTTGTTAGATAAAGGTACTTAAATATTCTATTCCTATATGAAGCCTGCCTTTTGGTTATGAACAGTATGCTTTGATGAGCATAAACAATTCTTAAATTATACCCAATACATGAGCCTCATCATTTCTGGCTACAGTGCCATTGGTGACAAATGATTCTTCTGTTGTTTATTAAACATTAAAGGTTATCTGTGACCTCCAGTATGAGTTATTCAACTGGAAGTTGTTGCCAATGCCAAGAAGCAAGAGAAGGAAATAAGAGATCCCTAGGCTGTAAGGAAGCAAATGAAGTGACAAGTCTCTGTAGTACATATAGTGAAACTGAAAGTGTGTTTAGAAAGGTGACACTATAAGCTAATATAGAAGGTCATTGGGTGCATGCATTCCACCACCAAGGAATTAAAAATTAAAATAAAAACACCAAGATACTTTGTGCGTATCAGACAAAAATGTAGAAGACTTGTATCTTAAAAAGTACAGATTATTGCTGACAAGAGCTAGACAGGTAGTGAAAGACTCTGAAAGGAGCCCCTTGCTCAGGCCTCAGGACAATAGCAGACACCCAAGAACTCACGATAGACCAAGCTTGATGTAAACCACATGAGGCTTTATTCGGGGAAAGCCAGAGCTCTGGGGATGACTCATATCCCACGCAGGGGTAGAGGAGTTGACCTCGAGGGGAAAGAGGTCCCAGTTTTTATAGGCCCTCAGGGGGGAAAGGAGAAGGGGGGAGTAGGGGATTTCCAGATCTAAACAATGTCTATTCTCAAGAAATGGGTATGGGAGGGTTACAAGGAAAGAGTCTGGTGCAGGTGTAGCAACTCAGGATTGGCCCGGCTGTGGTTGCTGGGGAGATTTTCTGATTCTTTCTCAGCAACCAATATCACAAACACCTGGCAATGGGCTTCATCAGGGGGCACACACATGGGTCAAGGAACGGTGAAAACATTGGCAGACACACGGGTTCAAGGAGTGGCCAGAGCATTATGCACCTCTATTTTTCTAAATCAGTGAAGCTAGTTCTGCTAACACTGACATCTGTCTTGCCAATTTCAGGGCTTCTGTGACCTTTTACATTCTGTCAGGATCTTTCAGTAGAAATACCATGTTTAAGGGTCGGAAGAATGAATACATGTGAATTCTATCCATATTTTGTAGATTCACACTCAGATAAATTCTATTAGTTTTTTTTGTTCATTTTGAAAAATGGATTCTGAAATTATATATACATGCAAATAACATAGAATTGCCAAAACAAATGTGGAAAAAAACCTAACAAATTGTAATTTAACATTATATTATTTTAAGATTTCATATAAATGCTTTAATAGCTAAGACAGTGTAAGTTTGGCATAAAAGAAATTGAAAACTCAGTGAAACAGAGAAGACAGAAATATTGCTTATATTTTATATATAATTAAATTTTCATTAAAGTTTAAAACAAAACAAAGACTATAAAAACATGACCTGTGATCCACTGTAGACAAAAGGAGTGGAGATGAGTCATACAGCCAAATACAAACTTAAAATGACGTAAACCCCAAAGAATGGAAAACAGGACAAATATTGGGAGACTCGATTAAACAAAAGTTTTCTAGGTATGACTCCAAAACCATGAGCTTTAACCGATTGAAAATCAGAGTCTCCTGCTTCTTGTCCGCCTGTGTGGCGCCTTTCTGTACTCGCTCACCCTCTCAGCTTCTGGGCTCGGCTTCTAACTTTGTTCCTTTTGTTCCACTTTATTTAACTTATCTTCAGATACCTTGGAGAGATAAATTTCTGTATTAATTTCCTTGACAACTCTTAGAAGTCAGTACACAGAAAACCTTCAAATATTTTGTATGTGCTTTAATTCTTAGTGTCAGAGCAAATCAATAACCGGTTTTTTACATTTCCTGTTATTCATATCACTGACTGTGTCTAGACTACCTTTTTTTTCTTTTTTTGTGTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTTTAAGACCAGGCTGGCCTCAGAAATCCGCCTTCCTCTGCCTACGAGTGCTGGGATCAAAGGCATGCGTCACCACACCCGGCTTATGTCTAGACTACTTAATCCACTTAAACTATGTTGGTAACTTTATGCACTGAAGTTTGCCTTCCTTAAGATTGTATGGAATTATGAAATACTTTATAGAGCTGAACAGATACATGCAAATTTGAGCCTTATTTTTTTCCATGAACTAG
Seq C2 exon
ATTTGTCATTTGACATATATGAAGGTCAGATTACTGCACTGCTGGGCCACAGTGGAACAGGAAAAAGCACACTGATGAATATTCTGTGTGGACTGTGTCCACCCTCTGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000018800-Abca5:NM_147219:11
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:
PF0000522=ABC_tran=PU(1.4=9.5)

							
A:
NA

							
C2:
PF0000522=ABC_tran=FE(25.2=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)
chr17:69291327-69294654 
LOW PSI
HsaINT0000708
(ABCA5)
Human
(hg19)
chr17:67287468-67290795 
LOW PSI
HsaINT0000708
(ABCA5)
Rat
(rn6)
chr10:98614337-98616790 
ALTERNATIVE
RnoINT0010276
(Abca5)
Cow
(bosTau6)
chr19:61888914-61889922 
LOW PSI
BtaINT0011106
(ABCA5)
Chicken
(galGal4)
chr18:8246432-8246846 
ALTERNATIVE
GgaINT0127840
(ABCA5)
Chicken
(galGal3)
chr18:7981923-7982337 
ALTERNATIVE
GgaINT0127840
(E1BY40_CHICK)
Zebrafish
(danRer10)
chr12:38655625-38658062 
LOW PSI
DreINT0023715
(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"