Special

MmuINT0007875 @ mm9

Intron Retention

Gene
ENSMUSG00000028125 | Abca4
Description
ATP-binding cassette, sub-family A (ABC1), member 4 [Source:MGI Symbol;Acc:MGI:109424]
Coordinates
chr3:121819573-121823037:+
Coord C1 exon
chr3:121819573-121819638
Coord A exon
chr3:121819639-121822947
Coord C2 exon
chr3:121822948-121823037
Length
3309 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
TTGGCGTCTGGTTGGTTCAGGTT
3' ss Score
5.99
Exon sequences
Seq C1 exon
GAGACTATGGGACCCCACTTCCCTGGTACTTCCTTCTGCAGGAGTCCTACTGGCTTGGTGGTGAAG
Seq A exon
GTAAGTTTGTTTTGTTTTAATTAAAACAGTCAGGCAGTGGAGATGCACACCTTAATACTAGCACCTGAGACGCAGAGACAAGAGAGTCTCTGTGAGTTCAGGACCAGTCTGGTCTATAGAGCGAGTTCCAGGACAGCCAGAGCTACACAGAGAAACCCTGAGCTGGAGAGATGGCTCAGTGGTTAAGAACACTAACCGCTCTTTCAGAGGTCCTGAGTTCAATTCCCAGCAACCACATGGTAGCTCACAACCGTCTGTAATAGGATCTGATGCTCTCTTCTGGTGTGTCTGAAGACAGCAACAGTGTACTTATATAAAAACAAACAAAAACAACAACAAATCAAGCAAAACAAAAATGAGAACAACAGAAACCCTTCAGGACTGAAACTACTTCCTTTCCTTGGGGTACATGTAAGATGTGTGGACCTTTGTCAAGGTGTCAAGGTGGCCCTTTGTCAAGTGCATGATCCCTGCTAGTCAGCTGCCTGCCGTGGGTACAGGGTGTCACAGTGTCACAGCCTCCACAAGTGTCCCTTTGATGAATCCCAGAGCCAGAGTAAATGGCAGAAACTTGACAGTTGGTCCTGGGAGATTGGATACTTGTTGAAAAGGGTGCACCATTTATTTCATAAGCCCAATACTCTTCCAACTTTCAAAGCAGAGATCTAGGAGGCACAAAGGGAGCTTTGCCTTCAGCTTTTGCTGCCTCCTTCTTCTCCGCCATGATGCCCCACATTCTCCAAACACACAGTAATTCACTCTTTGAAGCCAAGACGGAGGCTGCACGGTTGATCTCCAAGGCTTTCTTATGGTGGAAGAAGGCAAAAGGGACATTGGCTGACAATGCCTCCTAAGTACAATTTATCCTCCTTCCAAAAACAAAAACAAAACAAAACAAAACAAAAACCCAAAAAACAAACAAACAAACAAACAAACAAAAAAAAACAGGAGGCCTAGAATTTTCTAGAAGTCAGAAGGAAAACCTCATATCATAGTCTTGGAATTCTGAGAAGGCAGAGAAACTCCAGATCAGTGGCTGCCAACCTTTCCAAAGCTGCATCCCTTTATGCTGTGGTGACCCTCCCCAGCCATAAAATGATTTCTGATGCAACTTCACAACTGTAATGTTGTCACTGTTATGAGTTGTAATGTAAATATTTCTGGAGACAGAGAATTGCCAAGGGGCCTGGACCCACAGGTTAAGAACAATTTCTCTAGAGCTGTAAGCTACAGTCTCTCCCAGAACTGGGAGGCTCTGAAAGAAAACCCCCTGCTTTCCAGGGTTAGAGCTCACCCTTCCCCGTCCACACTTCACTTTGAATTACTGGGCCTGGGGCACGATTTAGCCTTTAAGCACTAACAAAGGGATTTAGTTTTCCTTTAACTTTAAATACCAGGTTAAGGCATTTAACCTGGAGCCTTTTAAAAGCTTGTATAAATTTTTGTTTGGCTGGTATTTTGAGGGTCTCCCCCACCCCCGAGGGGATATATATATATACATATATATATATTAATAGTTCACACAAACATTACTTTGACAGGCCAGTATTTTCCCATTATATTGTTTTGTGCATTGTGTTTATCTACAAACTTTTAAATGTCCACTATAACAAAGTTATCAACCTCTCTTAAATAAGCATATTTAACATCCCTGGAATGTTACTAATGTCAGTGAACCTAGGGGCTCATGTGCTCCCCAACCCCCACCCCACTATCCCAAGAGATACTCTGCTATTCAAGAAAAAAAAAAATCTTGAGAAACGTGTTCCTTGAAAACGAGACACATACACTTTCCTGACAGACGTAAAATACTTCTCACCTGTTTCATAGGCAAGAATAAATACAATCCCTCACACTATCTAAGATCAGAGAGCAGCTGAGTCACCCCCCTAACTCCCCTCTTCATAGTTGAAGAAATGGAGAGCCAGAAACATCAATTTCCTGTTGAAATCCCACTGGACACTGGGGCAAAATCTAGAATAGCCGAGGACGGTTCACGAGGAGAGTGTCACTCCAGTGGTTATTTAAAAAGATATTTGTTCTTGCTGCTGTATTACTCATGAGGGCAGTATGATAGCCGGGCAGTGTGATCGCCGGCACATTGACCTCGGAAATTGTGGAGAATAAAGTCAAAACTGCTTCAGGAAGTGGAGACAGAAGTACACCAGACAGCACTCCTCTCACCATTAAGCCTCAGCCTGCTGCTCTCCCACATTCTGCAAATCTAGAGGCCCTGTCGGGCACTGAGGATACTCCCTGGTGGTTCCCCATGTGTGCTTAAAGCAGAGCCCTAAGGGCTTGGTGCTAGTGGCTTTCTTTTCTTCCTGCTTCCTTTATGGCTGGGGCTCCTTTCTGCCTCTTCCTTTTCCAGGGTGTCCTTGACACCTCCTTAGACCGAATGCCATTAAAAAATAAAATCTGTGGTGAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAGGGGGGGTGTGGGGAGGAATAGCATACACCCACCAGGCTCCACCCTGGTATTACCGTAAGATTTCTGAATGTCCGAATAGGTGGCCTTTTAAAGGGAGCCATTTCTCCAGCTCAGATCTAAACTAGCTACCCACCATAGCACTACAGGTGGATTTTTGCTCAGGGCTCCCATGACTGACATGTTTTAGTTGGAGCAAAAAGGACCAGGTGGTAGGCTAAAGAAAACAAACCTATTCCAAATTTAATCCTGCGATGGATTTTTTGATTTGTCTGATTCCCCCACCCCCACCCCCTCAAGGGGACAACATTCAAGACAGGGTTTCTCTGTTTAGCCCTTGCTGTTCTGGAACTTGCTTTGTTGACCAGGCTGGCCTCGAACTCAGAGATCCACCTGTCTCTGCCTCCCAAGTGCTGGGATTAAAGGTGAGCACTGCTCAGCTTGTTTTTGTTTTTATTACAATTTCTGACATGAGCAGTCTGCCACATTAAAAGGAATTGCCGAGGACTGCGAATGTGGCTTAGTGCTACCAAGCAGGGAGTTCCTAGTTTGATTCCCAGTTCCCCCTAACAACAATGTAAATCAAAACTCTCCAGCTTCAAGGTTCTGATTTAAAAAGTCCCTGTGGGCCCTGCGAAATCGGCACAATCAGATTTGAGTCCCTCACGGCTGGGCAGCAGGTCAGAGCTGGAGGCCATGCAGGAGACGGGTCTCAGAGCTATGATGGCTCCAACCTCTGGAGGGAGCTGTCCCACCCTTGTGATGGGAAATGCATCTGTCCCCACTGCCCCTCCTCTTCTCTCCTGTCTCTCCTGAAGAGTAACGTTGGCGTCTGGTTGGTTCAG
Seq C2 exon
GTTGTTCGACCAGAGAAGAAAGGGCTCTGGAAAAGACTGAACCCTTAACAGAGGAGATGGAGGATCCAGAGCACCCAGAAGGAATGAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028125-Abca4:NM_007378:17
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.806
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000013995





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000013995f2261A, ENSMUSP00000013995f5872A, ENSMUSP00000013995f5873A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:94048958-94051632 
LOW PSI
HsaINT0000667
(ABCA4)
Human
(hg19)
chr1:94514514-94517188 
LOW PSI
HsaINT0000667
(ABCA4)
Rat
(rn6)
chr2:225720944-225724326 
LOW PSI
RnoINT0010233
(Abca4)
Cow
(bosTau6)
chr3:49622580-49625850 
BtaINT0011064
(ABCA4)
Chicken
(galGal4)
chr8:12641169-12645177 
GgaINT0034967
(ABCA4)
Chicken
(galGal3)
chr8:14391012-14395021 
GgaINT0034967
(F1N8D7_CHICK)
Zebrafish
(danRer10)
No conservation detected
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"