Special

MmuINT0042029 @ mm9

Intron Retention

Gene
ENSMUSG00000063681 | Crb1
Description
crumbs homolog 1 (Drosophila) [Source:MGI Symbol;Acc:MGI:2136343]
Coordinates
chr1:141219804-141224923:-
Coord C1 exon
chr1:141224728-141224923
Coord A exon
chr1:141219944-141224727
Coord C2 exon
chr1:141219804-141219943
Length
4784 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
AAATTTCATTTGCTCTCCAGTTA
3' ss Score
5.1
Exon sequences
Seq C1 exon
GCGTGAACTGTGAGTTGGAAATTGATGAATGCAGATCCCAGCCTTGTCTCCACGGTGCCACATGTCAGGACGCTCCAGGGGGCTACTCCTGTGACTGTGCACCTGGATTCCTTGGAGAGCACTGTGAACTCAGCGTTAATGAATGTGAAAGTCAGCCGTGTCTCCATGGAGGTCTATGTGTGGATGGAAGAAACAG
Seq A exon
GTATGTGTTGCGTAGATGACTGGTAGGCTTACAGAGACCAAGGTCTACTGTACAACTGTCGTGAACTTCAAGCTCTCCTAGCCTTCATTTGAGTCGTGAATTGGATTTTGCTTTAAGTAATGAAAAGTTACAGAATTCTGAGTTTACTTAAGAATATTTTTTGGTTGACATCTGTCCTGAGTGAAGGTTTTCCAAGGCATTCTTGTAATTGATTGAGAACTGTAGATATCAGAAAAGTACCAACATCCAAAACCCATGTAAAACCCTGTAGTAAACATCCTGATAAGGAAGTTGCAAAAGCAATGCTATCAACTGTTTAAATTGTGAACATAATGTTTATATTTATGAAAGTAAGCAAACCAATCAAATGGAAAAATAAATCCTTCGGAATTTGTCGATAAATACTCCTCTAAGGGCAATAGTATTAAATTGACATATCTTGGCTTTTTAACTATTTGGAGAATTGGGTGAATATATTTGACAAGGCATAATACCACCAAGTATAACTCAATTCTGATCCAAATGAAAGTCTCTCATTGGTTTCAGGGAAATGGGCAACTCTGCATTGTAGTATTTATCTTCATGTGATAAATATAATGAATTTATATAGTGAGAGCCAAGTTCACATCAAATAATATATCCCTGTAAAGAACATTGTCATATTTGCTTAGACTGTGAATATTGCATTATGGAGTGCAGAAAAATATTTCATAGCATTGAACTTAGAATTCCTTCCTTTGATACTTGCTCAGTGTGAAGCGTGCTGAGAATTACTGTTCTAAAGCTGTAATATATACAGTTCCTCAATTGTAATAATGAATCTGTAGTAAACAGAGGTTTCCAAGAGTTCACATCATTAATGTTTTCCAAAAGTAGAAACAAAATGACTTTTCCTCTATTTAATAAATCAGATATGTGGCTGAGGATGAAGTTCAGTGGTAGAGTACATGCCTAGTGTGTGCAAGGCCATGAGTTCAAGTCCCAATAGTGCATGTGTACACAACCTCCTCCCCTCCCCCCCCACACACAAAGAAACTCATAACTTCAAATCTAATTTCAAAATTACTGAAACTCAAAGAGTGCAAGAAAAGGCACGTGTGCTTCAGATATATCTGTAAGCTACTTAATAAGATAGTAATATTTTTAAATAGAGTAATAAAGTTGCACGTTTCTTTTTTAAAACTATGAAATGCCATTTTAAATCACAACCCATAATTTGATCTGACTTTTCCTAGCACTCAAATAATACGCCTTTGCTGGGAGTCTACACTCCTGGGGACAGCTTACTGGACACTTAGAGACAGAAGGGTTGGAATGGCTGAAACTTCCAAGGAAGTGAAAACCCTCTGCAGTGCATACTGTTCTTTCCAGAGAGCATCACAGCAGATAACACAGCGGTTTGGGTTCTCGTGGGAAGGCAAACACACTGGAAACTTGTGCTCGCTCGCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTCCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTAATTTACATTTCAAAAGTTATCGCCTTTCCTGGTTTTCCCTCCAAAAACCCCCTATCCCCTCCCCCTCCTCGCACTCCCCCCTCCACCAACCCACCCAAGAGGGAGTGCCTTTCATTCTCTACTCTTAAAGGTGAAATGACTTATTTCTTAATTTTATTGTTATATCTCCTAATACCTAACTTGGGAGAGGATTGAGATTATTTTTACACAATTAAAAATTAACATCTTTCCTATAATTCATGTGAGCAAATGGATGCTTGCATACCAAAGGAGCTTTTAAATGGAATCTTTAATTCTGTGAACTTAGATGCATTCCTTTAATATAGAACATGTGTCTGCAATACCGCACATAAAGTAGAGTTTAATATTTTAATCCTTATTGTTTATGGACATTCACGTGTGTGTGTGTGTGTGTCTGTGTGTGTGTGTCTGTGTGTCTCTGTGTGTGTGTGTAAGTTTGGGGATTAAACTCAACCCCCCAGGCTTGCACAGCAAGCGACTTCATGTGCTAAACATTCTTTCTAGTCCTAGTTTTTAGTATTTCTAATTACACAAAAACTATGAGCAGATTTTTTTAAACTAATTGAGTCATAAAAACCTTGTCCCTGCAACATCTGTCATTTCCAGATCCTTAAATAGTCCAGTATCAGTGCTTGGTGGTAAATATACACAGCCACAGAGACTGGATTATAAGTGTCCCGTGGTTGAAGCAGCCCCTCCAGATACCCTTTCTACCTCAATAAGTTTGCAGGCCCCGTTTTAATTTTTACAACCCTAAACTCTTGAAGAAAGAGGCATCACCTCAATTTAGAGCCACTTTAAATTAAAAACTCAACAATTATCCCCCAGTGGGTTGATTTGTGACACCGTGATTTAGATTTAGTCAATGAATGATTAGAAATAGAAAGACCCCTCTCTCACTACCACCACCATGGGAAAAGAGACACCTTGTGGATGGTGGTGTTCTTACATCAGTCAGGGCCAGAGCAGATGCCTTTGTTCATCCTGGTTTAATCCCTGCCTTGGTGGCCAAAGCAATGCCTAAGACTCATAAAAATCAAATCAAACCCAGGCAGCACAGTGTGGAAAGAGAAAGACAGAGACCTGTGCACCAAGTATGCCATGCTACCCAAAGACCTACATTCCATTGATTGATACAGGCAGGGCATAGACCCCTGCTTGCTGACACATCATGTATCACAGATGGAGGAAGTTACCCAGGGGCCTGGCAGCTACACACCTCAGGCTGCAGTGGGAGCAACCACGATGTGCGAGTGTGTGGTGGTCAGAGGTGAGAGTTAAAGAAGTGGAACAGCTTGAGCATCATAAAGACAGATGGAACTGGAAACTTGAGGGTGGAGAGGGATAGCCTGTTGTCAGTTGGCAGCCCTGCCACCTGGGGCCATGATGAGGTCCCAGCCAGAGTTGCCTCTGAGAACCAGGTTTGAATCCATGGCTACACAGCAGCAGAGGTCAGGGGTCTGTAATAATCTCTGAGGCTCATGCATGAAAATGTATGAAGCTCAAACATGGAAATGTCTCTGGTTAGGACAGCTGCCAGGGATCACGTGGATGTCTAGGGACTTCACATAACTGGCCCTGCCCCTCACAGCATGAAGGTCTCTGGAGAGCTGGCCCCATCTTTCACAAGCTGAGAACTCTGGCTAGTGGGCCCTGCACTTTACCTAAACAACACAGTAGAGTAGCTCCTGTTGGCTGAGGTGTGGTTGAGTCAGCCTTAGGGTTATGAGAACAGGAGAGCTGACATCACTCTCCACTCCTACATACCCTGCAGTAACCATGGAGAGCTGGCTCTGTGGTCATGAAAGCAGGAGACCTAGCCCTCTCCCCTCCTTGACTGTAACACTCAGAAGAGCAGGCCCTGCACTTCCCTGTGCAACAGAGTGGAGGTGGCCTTCATGGCCAAGGCACGGGTGAGCCAGCCCCAAGGGTAGCCCAGCTCTTCACAGGCTGCAGAACTTGGGAGAATGGGCACTGCACCTTGCATCTCAACTGGGCAGCATAGTAGAGCTGGCTCTTAGAAGCATGGGTACTGGTGAGCCAGTCCCAAGGGCATGTGAGCAGAAGAGCTGACCCTGCCACCTGCTTATGCCAGCATTGGGTGGCCTAGACAGAGCAGTGCTGGAGAGCTCACCCTGGTGGTACCAATAAAGTAGAGCCAGAGGTTTAACCAGCTCAGTTACTACCCAGGCCCAGATCCAAAGCTCTGAGTTGGCCCACCCCAAAATCTATATCATCTATGGATGGTTGGGATGCACAAAAAGATCAGTCCTGTTATTCCAAAGCTGCAGGATCTCCACGACAACAAGAGGATAACTGGGAGGAGTCCCAGTGAGGATTCAATATTGGTGGTGTCACAGAAGCCAAAGATCTGGAACCAGACAAATGACTCATTGCAATGAACATTTGCATGTGAAGATGTGTGGTTAGAAGGATATATGGTGGGACACATTGTGACATACTACAGTTTCCACCATGATATGTTTTCCATGCTTTGATTGTTTTGTTGTTGTTGTTGTTGTTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGGTGTGTGTGTGTGTTATTTTGTGGAGGATGGGCAGATATGAAGGAACAGTGAGATGTGCCGATGAGTGGGACTGTGGTGCATAATGTGAAACTCACAAAGAGTCAATAAAAGGTTTAAAAAAAGGAAATAGACTAAAATATTCATGTAATAAAAAATAACACCGTAATCATAATATACTTAATTATGAGTACTTATATTTATTTTACCATTCAATTGTAACCCAGTATCCTGATATACAAGGGATGATGCAAGAGATGGTGTTTCTATCCTTTATACATATTTAATTACCATAATAATCTCGCAAGTGTCATAGTATTATTTATGCCTGAAAAAAGTTTCCAAATAGTATTACATGAATCTTTTCATGTCACTTTTCAAGTCAATAATACTAAGGTGTTGATGTGAAAACACATAACCATGTAGGTCTACAGAGATAACTCCATGGTGCTTTTGAGGTAAGTATGAACGCTCCACCATCTGTGTCACGTTGATGGATAAATGGAGACAAGATAAAGGTTGATCTCAAGATGACCAAGAGTTGATGTGAAAATTTCATTTGCTCTCCAG
Seq C2 exon
TTACCACTGTGACTGCACAGGTAGTGGATTCACAGGGATGCACTGTGAGTCCTTGATTCCTCTTTGTTGGTCAAAGCCTTGTCACAACGACGCGACATGTGAAGATACTGTTGACAGCTATATTTGTCACTGCCGGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000063681-Crb1:NM_133239:3
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:
PF0000822=EGF=PD(6.5=3.0),PF0000822=EGF=WD(100=47.0),PF0000822=EGF=PU(54.8=25.8)

							
A:
NA

							
C2:
PF0000822=EGF=PD(41.9=27.1),PF0000822=EGF=PU(78.1=52.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000060769





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000027616, ENSMUSP00000118324, ENSMUSP00000120391, ENSMUSP00000123136
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:197344477-197347339 
LOW PSI
HsaINT1008378
(CRB1)
Human
(hg19)
chr1:197313607-197316469 
HsaINT0041232
(CRB1)
Rat
(rn6)
chr13:56408286-56413440 
LOW PSI
RnoINT0041818
(Crb1)
Cow
(bosTau6)
chr16:78176410-78179239 
LOW PSI
BtaINT0043700
(CRB1)
Chicken
(galGal4)
chr8:2529839-2530961 
ALTERNATIVE
GgaINT1010430
(CRB1)
Chicken
(galGal3)
chr17:9705826-9706152 
LOW PSI
GgaINT0126096
(CRB2)
Zebrafish
(danRer10)
chr22:23497494-23499417 
LOW PSI
DreINT0051762
(crb1)
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"