Special

MmuINT0137348 @ mm9

Intron Retention

Gene
ENSMUSG00000039087 | Rreb1
Description
ras responsive element binding protein 1 [Source:MGI Symbol;Acc:MGI:2443664]
Coordinates
chr13:38038726-38043871:+
Coord C1 exon
chr13:38038726-38039532
Coord A exon
chr13:38039533-38040511
Coord C2 exon
chr13:38040512-38043871
Length
979 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
TTCATTCTTTCATTGTTCAGGAG
3' ss Score
8.33
Exon sequences
Seq C1 exon
ACAGCCAGTCAGACACAGACACGTTGACCACCCCAGGTGAGGTGCTGGATCTCACAGCACAGGCTAAAGAGCAGCCGCCAGCAGAGGGAGCCAGTGAGATCAGTCCGGCTTCACAGGACCTTGCTATCAAAGAGGCCAAAGCAGCAGCAGCTCCCTCTGAGGAGGAGGAAGAAAAGGAGACAGAGGAGAACCCAGAGCCAGAGGAAGAGTGTCGTGTGGAAGAGAGCACTGGGGCTGCAGATGCCCCCGAGGAAGACACAGCCAGCAACCAGAGCCTGGATCTTGACTTCGCCACCAAGCTGATGGACTTCAAGCTGGCAGAGAGTGAGGCAGGCTCTGTGGACAGCCAAGGCCCAGCCCAGCAGGAGCCAAAGCATGCCTGCGATACCTGTGGAAAGAACTTCAAGTTCCTGGGCACCCTGAGTCGCCACAAGAAGGCACACAGCTGCCAGGAGCCGAAGGAGGAGGAAGCAGCGGCACCTTCGCTGGAGAATGAGGGCGTTGGCAGAGCGGTTGAGGGGCCCTCGCCTTCCCCTGAGCCTGAAGAGAAACCAGCCGAATCCCTAGCAATCGATCCAACACCAGGAACCAGGGAGGCCTCAGTGGCGAAACAGAATGAAGAAACAGAGGGTCCCACTGATGGGGAAGGTACGGCTGAGAAGAGGGGTGACGGTGACAAAAGACCAAAGACAGACTCCCCCAAAAGCATGGCCAGTAAGGCAGACAAGAGGAAGAAGGTTTGCAGTGTATGCAACAAGCGGTTCTGGTCCCTGCAGGACCTCACCCGGCACATGAGGTCACACACAG
Seq A exon
GTATGAGAGACCAGAGCCAGCCTGCCAGAAGAGGTGGCCTGCAGTGGCCATTGGGAGTCTCCCTGGAAGTCAGGTCCAGGGGCCACTGAGAGAACTGGCTAGGTTGCAGGGTTATCCTCTGACCTGGGAAGGCTGGGGGTCCTAAGGAGGTGTCTCCATGGCCTTGGAATGCCACAAGCCTTCTACAGGGCAGTGGTCCCTCTGCAGTAGTACTTTGGAAAGCATTTTTCTTCAGCCACTCAGCCCCAGTTTTGTCCTCTATAGATAGGGAAGGTGGCCGCCCTGTGCACAGGTTTCTAAGAACAGGAAGAATAGGCGGATGTCCATCTGGTGTAAGACTCAGCCAGATCCTGAGAAAGACAGGGATATGCCAGGGAAGGCAGGTACTGGCCTACACATATAGGGAAGGCCCCAAAGGGTCTGTTATTTTAGTGGGGGGCAGGGGTGGGGGACCTGGGTAGAACCATGAAGCCAAAAGGCAGAGACACCCTTCCTCGGCCATCCCTCCAAAGAGAGCACCTCCACCCCCTGACCACATCTCACCGTCATGGCCTCCCGTGCACAGTGGCCGTGCCACAGCCACTGAGGTGTAGCGTGCTGGCACTTGTTCTGGCCAGAGACATTGTCAGCTGTTGAGAGACTTGGTCCGTAAGCTGTCGGGAACATCCAAATGCATCCTCCTCATGCCTTGCTTTAGGTGGCTGTCCATGGCCTTGCAGAGCCCAGGGGAATCATTTCTCCTAAGGACGCTTTGCTTCTGGGCTTCTCTTACGATCAGTTTGTAGAAAAGCTAGGCTGAGAGGTACAGGAAGAAGAATGTGACACCCCCACCCCCCCCAGCCTTGCCAGTTTGGACAAATAAGAGAGTCCTGTCCCTGTGTATTTAGTTCTGGATGCTGCATTCATATAGAGTGTGGGAGGTGGGAACCAGTGGCCTTTGTGTTAATGGACGTCTCCCTTTCATTCTTTCATTGTTCAG
Seq C2 exon
GAGAAAGGCCATACAAGTGTCAGACCTGTGAGCGAACCTTCACCTTAAAGCACAGCCTGGTTCGACACCAGAGGATCCACCAGAAAGCCAGGCACAGCAAGCACCACGGGAAAGACAGCGACAAGGATGAGCGGGCTGAGGAGGACAGTGAGGACGAGTCCACCCACAGTGCTACCAACCCTGCCTCTGAGAATGAGGCCGAGTCAGCTCCCAGCACCAGCAACCACGTAGCTGTCACCAGGAGCCGGAAAGAGAGCTTGTCCACTTCTGGGAAGGAATGTAGCCCAGAGGAGAGAGCCGCAGCTGAGCAGGCAGCTGAGCCCAGTGCCCCCAAAGAGCAGGCGTCTCCAGGTGAAACAGACCCCCAGAGCCCGGCAGCCATCGTGCAAGACTTGCTGGAGCTGTGCGGCAAGAGGCCTGCCCCAATCCTGGCGGCCACCGACGGGGCCTCACAGCTCCTGGGCATGGAGTGACAGCCCGCCCTGTCTCCATCAGCTCAGAGACAAAGCTAGCGGAGCATCCCAAATGTAGATTTTACAAGGTTTTCTCAGCTTCCTTCAGTTGTCTGGAGAGAGAGGAAAAAGAGGGCAAGAGAGAGACAAGCAAGCCTGTGGCCAACCAGCTCGTGCCATAGCCTTACCCAGTACACATGCACCCGGCCCCAGTACAGCCGGCTTCAGTGCCTTAACTACTTATGGGTCCTCCCATGTCGTTGTGGGTGTCCCCCTTCCAAAAAAAAAAGACATTTTAACAAAACAAATATTTTAATGAATTTTTCGGAGGACCTTTTCATTTAAGCATTAACATTACCTTTTGTATTTGTGTGTTTGAGCTTGTTTTTGTGAGTCTGTGATAGTACTGTTTTTGTTCTGTGAGCTGGAAGCAGAAAACCTTCCCCTTGGATCCTGTAGCCAATAACTGGAAGAAAATGATGTGAATTTCATGTACATGACCCGAGGGAAGAGGGTGTGAGGCTAATTTCTAAGCTAGACCTGTATTCTCTGGTTCACGTCGGGGAGGAGCCGCGGCCTGGCCTCTGTCATTAGTAGATGTGGTTGACGCAGGGTTCCTGTGTGGTGTGAGCCAAAGCCAGGAAAGAGTCTAGCTTCAACCTCGCGAGTGTTTCCACCCTCTCCGTGTTAGAAATGGCTAGTGTTCCCATTCTTAATTTACAGAGAAAAGTGGCCTCCCCAGCACCCTAGCCTACAGAGGACACGGCTGGAGGTCATATAGCCACTTTCCCTTCTTCCCATTCGGTATATGTTATTAATATTATTATTATTATTTTTATTTTTACTTCTTCAGTTCGCTGGGCTCTGCATTCAGCAGAAACAAATGGGCAATATTTGTCCTGGGTGACCTGTACTGCTCCCTGGTCCCCCCTTATTGTGTGCCTGAAGCTTCTGGTGGCACGCCAGTGATGGCTCTTCTACTGTACTCAGACAAACCTTTCTTCCATGACTGTAGAATCCAGCAGGGGCCAGGAGTGGTCCTCCAAGCGTGGCCAAGGAGTGGCTCAGAGGGGAGAGCAAGGATGCACAAGTGGTGGGGAGCAGGCATCCGAGACACCAGGCCATACCTGGGGCACCTCAGAGTCAGTTTGCAAGGCACCCCAGTCTTCCTGCTAAGCTGGGTCAGCGCCTTCCCCCAGCCGTGCTACTACCGTCATTTGGGAAGCATTGAGATACTACTGCCAGTGATGAACTGAAGTGCATGCGCAAGGTCTAGATGCGAGAGTTGTCTTCACCTTTCTGCAGTGTGGGGTTGCTGCTTGGAGAGAGGAGTGCTTTTAAATCCCTAACTGGCCCAAGCCCCTGGTGCACAGAGACAGGGTTCCTTTAGTTCCTGGGTGTTCTGTACAAACAGTAGACCTCGCTCATCAGCAAAAAGAAACTCTTCCTACTGTAGCTGAGCTCGGTTCAGCACCCTGTCCTTTAGCCGAGACCCGAGGATGCCTGAGCCACACTGCTACTAGAGCCCTGTTTGTCCCTTGCCTTCAGGGCCTCAAGATTTCCCCAAGAGAGGCCCTCCACTGCTTCACCCCCTCCCTTATCCTGTGGCTCTATATGCTCCTCCGCAAAGATGTGCAACCCGAGGCGTGCGTACCCCTTTGTCCACCAGTATCTAGTGGCTAAAATCCAACCACCCTGACTTCAATGGAAGATAGATATTCTAGAGATAATGAAAAGTGATATATGTATGAAAAAAACATTGAGGTATATATGATTTTTAATTGTATTAGGGATGTGTGGACCCATTTAAAGTTGAGATTTTATTTACTGTAGAGAGAGAAAAATCAGAACCATTGATCCCATGATCTTCTAAGTCAAACCCAGCTCCTACATCCCTTAGGTGTTTTTATTATTATTATTATTATTATTATTATTACAATTGTTATTGTTTTCATTGTTATTATTTGGGGTTTCTTGTGTTTTGGTTTTCTTTGCAACTCTCCACACTAAACTCATGATACTGTGGGGAGAGGCCATGACTGAACCCTACGCTGCGGTAAGATGTAGCAGGGGTTGCTCCCAGCAGCGGCCGCCGCCAGGGCTGCAACTGGCAATAATCACTATTGATTTAAAGCTTTATTTAGTCTCATCTGTTCCTTCATAGTTAATAAGGTCTTGCCACATTTTATTAGTGAGATTGAGAGATGAATTATTTGTCTGTTGTCCTCCCCGCCTTCCCTCCCCCAATATTAAACTGTGAAGTTTGTGATTTTGTTTAAACGCTGGGTGAATCATAGTGTTAGTTTGCATGTCCAGCTAATTTGTTTCTATACATTTTGTTTGATTCTCTTTCTCCTCAGGGCTTTTACAAATATATATATATTATATATGTATATATATATGGATCTTCTGAAAAAAATTGAGGTGCAAATTTTCTCTTTTTTGTTGTTTTTTGTTTTCTCTTTAATGGACACAATGCTGATATTCAATCACTACATAAAATATCTGGCTGTGAAACAAACCAGAGAGGCCCCACGGGGCGTTATCCAAGCAGCTCTGCAGAAGCTCCGTGAATCGGATACCGATTTCAGACAGATCATCCTGCGTTCGTCTCTTTCCTCTCTTCTCTTTCTTCAAGAAAAAAAAGTTGATCCTAATGATTTCAGCCCATGCATTAAACAGAAAACAATAATAACTGTAGAATTCATATTTTTCTAAAGGGAACTTAAAAACTGCTGCTACATGTATGTACAAAACTGGTCTCTGCTACATGAACAGAATCACAGGTTTGGTTTTGGTACTTTTGTTTCTCTTTGTACTCAGTTGTGTAGAACTTCCAAATTCAGAGTGAAAAGAAAGCTGTTCTGCATCAAACCATCTAAGCAATAAATGTTATATTTAAAAAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039087-Rreb1:NM_001177869:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.926 A=NA C2=0.970
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0009621=zf-C2H2=WD(100=8.5),PF134651=zf-H2C2_2=PU(40.0=3.7)

							
A:
NA

							
C2:
PF0142811=zf-AN1=PD(82.5=20.9),PF0009621=zf-C2H2=WD(100=14.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000115599





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000049265, ENSMUSP00000124802
  



Associated events






Conservation


Human
(hg38)
chr6:7247222-7248510 
LOW PSI
HsaINT0143330
(RREB1)
Human
(hg19)
chr6:7247455-7248743 
LOW PSI
HsaINT0143330
(RREB1)
Rat
(rn6)
chr17:27542446-27543417 
ALTERNATIVE
RnoINT0129326
(Rreb1)
Cow
(bosTau6)
chr23:47901107-47902161 
LOW PSI
BtaINT0127292
(RREB1)
Chicken
(galGal4)
chr2:64735933-64739400 
ALTERNATIVE
GgaINT0096712
(RREB1)
Chicken
(galGal3)
chr2:65835054-65838521 
LOW PSI
GgaINT0096712
(RREB1)
Zebrafish
(danRer10)
chr2:21400007-21401901 
LOW PSI
DreINT0129313
(rreb1b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GAGCCTGAAGAGAAACCAGCC

				
R: 
TCTGGTGGATCCTCTGGTGTC

				
Band lengths: 
355-1334

			

		

	





	
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"