Special

MmuINT0048207 @ mm9

Intron Retention

Gene
ENSMUSG00000035392 | Dennd1a
Description
DENN/MADD domain containing 1A [Source:MGI Symbol;Acc:MGI:2442794]
Coordinates
chr2:37654510-37657793:-
Coord C1 exon
chr2:37657535-37657793
Coord A exon
chr2:37656771-37657534
Coord C2 exon
chr2:37654510-37656770
Length
764 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
TCCTCCCTCCTTCCCCACAGAGA
3' ss Score
11.87
Exon sequences
Seq C1 exon
GCCACAGCCATACCGGACATTGAAAGAATCAGACAGCGCAGAAGGTGATGAGACCGAGAGTCCAGAGCAGCTAGTTCGAGAACCCTGGGGACCTACCCCTGCTCCACCTGACCGAGCTGCCAGCATTGACCTTCTAGAAGATGTCTTCAGCAGCCTAGACGTGGAGGCACCACTGCAGCCGCTGGGCCAAGCCAAGAGCCTGGAGGATCTCCGGGCCCCCAAAGACTTGCGGGAACAGCCAGGGAGCTTTGATTACCAG
Seq A exon
GTATGATGGGAGTAGGGAACAGTAGTTGATGGGGTGTCTCCTAATGAGCAAGGTCCTCCTAGTCACAGTGGAAGGGGCCAGGGAGATAGGACATCACATCCCCACCCCTGTGTTAGTACTCCAACCCCACCCAATTTGGAGCAGTACACTGTTACCAGCTATCACGGGGAGCTATCTATCATGCTAGCACAGCAGGGGGTGTCTGCCTGCCTCCATTCTTATCTGATAGTTGGCTGCTGCAAGGCTTGTCCAAGCCCACCAGGCTCCTTGGATCAAACTCCTGGGTTATGGATTGGTTCTCCCAGTGCGACTATCAGTCAGCTCCCCTCTCTGGGATTCATAGATTATCCCACCTTCTGGGAATGAAGCAGCTCTAGTCTAGCCCAGGTCAAATGGAGGCATGGTCAGGACTCAAATACAATCTCTTCTCTGGCTCCTGTCCCTTCAGCCAGGCCTAGAGTTACACTTGCCCCTTTGAGGGTAATCAAAGACACCACAATCTCTGAACAGCAAAAAGGCTCAAGCCATTGTTAGGTGGCCCACAGATGGAAACATTTTCCTGAAACTGCTTGGCAAGCATAGGCATTTGTAAAAAGACAGGAGATTCCTTTGTATTCCTTTTGTGGAACACAGTAGGGCTTGGATCTCTGCAGGTGTCTTGGGTACCTGCAACTCCTCCCAGTCCCAGGAGCAATGTGCTTGGCATGCAGGAAGGGTTGCCTGGGCTAACCAGTGGTCATCACTTCCTCCCTCCTTCCCCACAG
Seq C2 exon
AGACTGGACCTGTGCAGAAGTGAGAGGGGCCTTAGCATGGCTGCAGCCTTGAAGCTTGCTCATCCATATACTAAGCTCTGGAGTCTGGGTCAGGACGACATGGCCATCCCCAGCAAGCCCTCCATAACCTCCCCTGAGAAGCCCTCAGCTCTGCTTGGTACTTCCCCAGCCCTGCCTCTCAGACCCCAGAACCAGGAGGGCATCCTGAGCCCCAGCATCAAGGAGGAGACTCCCATCCCAACTCCGGGCAGCATCACCATTCCCAGGCCACAAGGCAGAAAGACCCCTGAGCTGGGCATCGTGCCTCCACCACCCACTGCCCGGCCAGCCAAGCTCCAGGCTGCTGGCGGCCCACTTGGTGACTTCTCTTCAGAGCCACTGCAGATGGACCGGGAAAGACAAGCCGCTCTGAGTCCAGCCCTCCTGTCAGGGCTGCTCCCCAGAGCTGTCCCCCAAGGTCCCACAGAACTTCTGCAGCCACCCAGCCCAGCCCCAGGAGCTGCAGGCACAGGCAGCGATGCCCTGCTCGCTCTCCTGGATCCACTTAACACAGCCTGGTCAGGCAGCACCATCCCATCACATCCTGCTACCCCCAGTGCAGCCACCCCATTCATCCCTCAGCTCAGCTTCCCCCCAACAGTGACACCCACCCCTTTTGTACAGACACCACTCAATCCCTTTGTCCCATCTGTGCCAGTAGTACCACCCTCCATGCCCCTGAGCTCTACACCAGCCAGGCCTTTTGGGACCCCTCCAGCATCCCTAGGGCCAGCATATGCACCTAGCATTCTATTGTCTAGTTCTGGCTTCTATGCCCCTCACAGGTCTCAGCCCAACCTCTCTGCTCTCTCCATGCCCAACCTCTTTGGCCAGATCCCAATGGGTGCCCACACTAGTCCCCTGCAGCCACTTGGCCCCCCAGCCGTTGCCCCCTCCAGGATCCGAACATTGCCTCTGGCCCGCTCAAGTGCCAGGGCTGCTGAGGCCAAGCAGGGGTTGGCCCTGAGGCCTGGTGAATCCCCACTGTTGCCTCCCAGACCGCCCCAGAGCCTACAGCCAACCCCGCAGCCCTCTGTTCCTACACAGGCCAGAGACCCCTTTGAGGATTTGCTGCGAAAAACCAAGCAAGATGTGAGCCCAAGCCCAGCCCCGGCCCTGGCCCCAGCCTCCACCTCCGTGGAGCAGCTCCGCAGACAGTGGGAGACCTTTGAGTGAGCAGGCCTGTGCCACTGTCTAATACTGTGCCTCCCCAACGTCCCATTTCTAGCCAGGCTTCATGGGGCAAAGGGACTCTGCCCCCTCCTCCACAGCCCATCTCTGAGGCCTGGCCCTGGGAATGGCCATCCCAGAAGAGCTGCCTGCCGCCACCCTTGGCACCCTGTGTGGGTTTTGCACTATATGTCAACTGGACCAGCTGTATCCTATCCTCCCATAGCCCAAGAGGAGTCAAGAAGCTCAAGGCTGCTTTCAAGCCCAGCTCTCCTCCTTTGCTGGGCCCCACCCCACAGGGCAGATGTCAGTAACAACCTGTGTAAGCACAGCTTTGGGGGACATGGGTGTTTGGGGGGCTGAAATGAGGCCCACTCCTAGGCTGGCATTTCTCCCTGGTGGTCATCTCCAAACCTCTCTAGCAATATACTCTTTCCTGAGTCTTCACCTAACCACCAACTGGAGTTGTTCCTGAAGGGTCAGGGGTCTGGAGACCTAATGGTCAGCAAACCCAGCCCCAGCCAGCTCTTCCAGGGGTTGGGAACACCAGCAACTCTAACTTATAAGAGAAGCTCCAAACCTGAGTCTTAGGAGCCGCCCTCAGCTCTCTGCCACCCTCATACCTCTGGGCTCTCGTGTCAGTCAAAGCTCAGGCCCAGCCTCCTGCCACTTGGAGCTTTATGGGCAGAGCTGGGCAGCAGTGACCCAGATTCCAACTCAAAGGACAAGCTTCCTGCCACAGACAAAGGGAGGGAGGCACAGCTGTTAGAGCTCCTGGGTCAGGACCAGGTGGGGCCCCAGGGCTCCCCAGGTTCCCCCATGGAGTGAAGATACACGTGGCCTCTGAGCGTGCGGCAAGTGGGGGCCTGGAAGCCAGCCCTCCCCACTCTCTCCAGCTTCTCGACAGCGCAGAAATTCCTGAGCCCAAGTCACCAAAGTTATAATGAAATGTTTTGTTATTTTTTCTTTGATCTTGCTTTTCCTTTTTACCTTATTGATTTGATGAATCTTGAAAATTGATTCCTTTCAATAAACCAAGGTAAAACACAGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035392-Dennd1a:NM_146122:21
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.874 A=NA C2=0.802
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000099848f6225A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000047498, ENSMUSP00000088520, ENSMUSP00000088520f3401A, ENSMUSP00000099848, ENSMUSP00000115527
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr9:126144905-126145933 
LOW PSI
HsaINT0046685
(DENND1A)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr11:94528757-94529997 
ALTERNATIVE
BtaINT0048014
(DENND1A)
Chicken
(galGal4)
chr17:9024408-9025059 
LOW PSI
GgaINT0124173
(DENND1A)
Chicken
(galGal3)
chr17:9737411-9738062 
LOW PSI
GgaINT0124173
(DENND1A)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CGAGAGTCCAGAGCAGCTAGT

				
R: 
GGGCTTCTCAGGGGAGGTTAT

				
Band lengths: 
349-1113

			

		

	





	
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"