Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttggttctcctctgttactgagttattaaatcattgtaaaatcgatgttctctatgttaaaaactcccgcgtatacaacacacag

Basic information

species Arabidopsis thaliana
transcript AT3G57330.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os12g04220.1 (Oryza sativa), 5'ss of exon 4
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttggttctcctctgttactgagttattaaatcattgtaaaatcgatgttctctatgttaaaaactc---ccgcgtata-caacacacag------------------------------------------------------------------------------
  | |  ||||| ||| | ||||| || ||||| |||||||||||||||||||| || || || || ||||| ||||| ||||| || || ||||||||||||   |||    ||   | |||    | |||| ||   |   | || | ||  ||    | || | | | |     ||  |||  ||  |  ||                                                                               
GTTTGATGAGGTGGTTTCTGTGACAGGTGATGGTACAAATGATGCTCCTGCATTACACGAAGCAGATATTGGGCTTGCTATGGGCATTGCAGGAACAGAGgtactgttt---cctatgcagttcaaaacttatgaacgtagcatcaa-tagacattaaaaaagtcagatatttaggacgaatatgtcagtattcactcttactgaattaagttgatcctgataatccatttttcatcttctgaaatggagtaattttgtcttgtatttgtgcag

upper sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os11g04460.1 (Oryza sativa), 5'ss of exon 4
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttggttctcctctgttactgagttattaaatcattgtaaaatcgatgttctctatgttaaaaactc---ccgcgtata-caacacacag---------------------------------------------------------------------------------------------------
  | |  ||||| ||| | ||||| || ||||| |||||||||||||||||||| || || || || || || ||||| ||||| || || ||||||||||||   |||    ||   | |||    | ||||  |   |   | || | ||  ||    | || | | | |     |   |||  ||  |  ||                                                                                                    
GTTTGATGAGGTGGTTTCTGTGACAGGTGATGGTACAAATGATGCTCCTGCATTACACGAAGCAGATATCGGGCTTGCTATGGGCATTGCAGGAACAGAGgtactgttt---cctatgcagttcaaaacttatggatgtagcatcaa-tagacattaaaaaagtcagatatttaggacaaatatgtcagtattcattcttactgaaataagttgaccctgataacccattttggatactttgtattttctttttcatcttctgaaatggagtaattttgtcttttatttgtgcag

upper sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G104730_T02 (Zea mays), 5'ss of exon 5
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttggttctcctctgttactgagttattaa-atcattgtaaaatc-------gatgttctct-atgttaaaaactcccgcgtatacaac-acacag------------------------------------------------------------------------
  |  | ||||| ||||| ||||| || ||||| || ||||| ||||| ||||||||||| || || ||||| ||||| ||||| ||||| ||||||||||||     |    |||     ||     ||| |||   | | ||||||| |        | |   ||  | | ||| ||||||  |   | |||   ||  |                                                                        
GTTCAGGGAGGTGGTTGCTGTGACAGGCGATGGTACCAATGACGCTCCAGCATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaactatacctcgcaatttctactgttcttactgtgaatgtaaaaacctcttgcaaggccatcagaagctaagaactcct-cacttgcaattgcaaggccatcatgcccttcggcaattctgtgcgtcccttgaaaagataaataacagtataagcttacatacttgcag

upper sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G357620_T01 (Zea mays), 5'ss of exon 4
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttggttctcctctgttactgagttattaaatcattgtaaaatcgatgtt----ctctatgttaaaaactcccgcgtatacaacacacag--------
  |  | ||||| ||||| ||||| || || || || ||||||||||| || |||||||| || || || || ||||| ||||| ||||| ||||||||||||    | | || |  | |   | ||  | ||  ||| |  |  | |   | |||    ||||||| |   |      |   | | |||  ||          
GTTTCGCGAGGTGGTTGCTGTGACAGGTGACGGCACGAATGATGCTCCAGCGTTGCATGAAGCAGATATCGGCCTTGCTATGGGCATAGCAGGAACAGAGgta---ctggattattatgtcgcattggttcat-gaatgacagggatacataggttgtgactctatgattcgagagttggtcaaaataacctacctagtaattt

upper sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G305159_T02 (Zea mays), 5'ss of exon 5
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttggttctcctctgttactgagttattaaatcattgtaaaatcgatg--ttctctatgttaaaa-actcccgc-gtatacaacacacag------
      |||||| || ||||| ||||| |||||||| |||||||| || ||||||  |||| | ||||| || || ||||||||||| || || || ||||||    || |   | || ||   |||  ||    | ||  | | |   | | |  |||   |||  |||| |||  |   | ||| | |    ||      
GTATCAAGAGGTGGTGGCAGTTACTGGTGATGGAACCAATGATGCCCCAGCATTGAGTGAGTCAGACATAGGTCTGGCCATGGGAATTGCCGGCACTGAGgtatgtcttcgagtttctatgc--ctgccttgcgtactccctctgattccaaaggattcatcatggaaaaatactttcatagcatatagctttgagtaattc

upper sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G15800.1 (Glycine max), 5'ss of exon 4
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgta---gcctttggttctcctctgttactgagtt--attaaatcat-tgta--aaatcgatgttctctatgttaaaaactcccgcgtatacaacacacag
  | || ||||| || || || ||||| |||||||| ||||||||||||||| |||||||| | |||||||| ||||| ||||| |||||||||||||||||    |||  || ||    |    |  ||  |   |    || |  ||||  |  ||  ||| || | | |    |  | |   | ||       |   
GTTTGGTGAGGTTGTAGCTGTTACTGGTGATGGAACCAATGATGCTCCTGCACTGCATGAGTCAGACATTGGGCTTGCTATGGGCATAGCTGGAACAGAGgtttgtgcccatgattgatttactatggtgtatctgacggtattacgtgtagcagttcattgtactgtttttgcttagttgcttggcatcttgtttaaga

upper sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA03G29010.1 (Glycine max), 5'ss of exon 5
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttggttctcctctgttactg-agttattaaatcattgtaaaatcgatgttctctatgttaaaaactcccgcgta----tacaacacacag--------
  | || ||||| ||||| || ||||| |||||||| |||||||| |||||| ||| |||||| |||||||||||||| ||||| ||||| ||||| |||||    | |   |||  | |  || |    | |||    || |    | | | | |  | | ||||||   |||| || |     |  || | | |         
GTTCGGTGAGGTTGTTGCTGTTACTGGCGATGGAACTAATGATGCCCCTGCACTGCGTGAGGCAGACATTGGACTTGCAATGGGCATAGCAGGAACTGAGgt---ttgtatctcttgtgtactattatgataattctgacagttacgagttgttttagttt-tgttaatt-ctcctgcattatgttttaagatataaggtgttat

upper sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA02G32780.1 (Glycine max), 5'ss of exon 4
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgta---gcctttggttctcctctgttactgagttattaaatcattgtaaaatcgatgttctctatgttaaaaactcccgcgtatacaacacacag-------
  | || ||||| || || || ||||| |||||||| ||||||||||||||| |||||||| | |||||||| ||||| ||||| ||| ||||||| |||||    |||  || ||    |    |  || ||  | |    |||  |   | |  ||||| | |  |       |     |      ||    |       
GTTTGGTGAGGTTGTAGCTGTTACTGGTGATGGAACCAATGATGCTCCTGCACTGCATGAGTCAGACATTGGGCTTGCTATGGGCATATCTGGAACTGAGgtttgtgcccatgatttgtttactatggtgtgtc-tgatggtatta-agtgtagcagttctttgtactgtttttgctttgttgcttggcatcttgttttttc

upper sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA19G31770.1 (Glycine max), 5'ss of exon 2
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttggttctcctctgttactgagttattaaatcattgtaaaatcgatgttctcta----tgttaaaaactcccgcgtatacaacacacag----
  | || ||||| ||||| || ||||| |||||||| ||||||||||||||| ||   ||||| |||||||||||||| ||||| ||||| ||||| |||||     |   || |   ||   |      |   |  | | ||||   |   | || | ||    |  || |   |       ||| ||  |        
GTTTGGTGAGGTTGTTGCTGTTACTGGTGATGGAACTAATGATGCTCCTGCACTGTGCGAGGCAGACATTGGACTTGCAATGGGCATAGCAGGAACTGAGgtttgtatctcttgtttactacgataattctggcagttaagtgtacgcttagttttgtataatagtcctacattatgttaaagatataaggcgttagcgt

upper sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA09G35970.1 (Glycine max), 5'ss of exon 4
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgt-agcctttggttctcctctgttactgagttat-taaatcat--tgtaaaatcgatgtt-ctctatgtta--aaaactcccgcgtatacaacacacag-
  |    ||||| || ||||| ||||| ||||| || ||||||||||| || |||||||||||||| ||||||||||| ||||| || || || |||||||| ||  | |  ||   | |     ||   | || |   ||||    ||  ||  || ||  ||  ||  |    |  |   | |  | |     |    
TTTTAATGAGGTTGTGGCAGTAACTGGTGATGGGACCAATGATGCTCCAGCTTTGCATGAGGCTGATATTGGACTTGCTATGGGTATTGCAGGGACAGAGgttagtttgttattacacccacactctatataatatccttcatgacttaccatttatattgttccgtgccatctgagattatgtgctttctttgtatctt

upper sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA12G01360.1 (Glycine max), 5'ss of exon 5
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttggttctcctctgttactgagttattaaatcattgtaaaat--cgatgttctctatgttaaaaactcccgcgtat-acaacacacag-------
  |    ||||| || ||||| ||||| ||||| || ||||||||||| || |||||||||||||| ||||||||||| ||||| || || || ||||||||    |||| | || | |    | |   | || ||||| ||    | |  | || |  || |||  |         ||||   |  |    |         
TTTTTATGAGGTTGTGGCAGTAACTGGTGATGGGACCAATGATGCTCCAGCGTTGCATGAGGCTGATATTGGACTTGCTATGGGTATTGCAGGGACAGAGgtt-tgtttgttactacacccacattctat-ataaaatccttcatgacttaccatttgttccatgccatctgagattgcgtgccattatctgcttgccttgt

upper sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv08s0007g08960.t01 (Vitis vinifera), 5'ss of exon 4
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttggttctcctctgttactgagttattaaatcattgtaaaatcgatgttctctatgttaaaaactc-ccgcgtatacaacacacag---------
    || ||||| ||||||||||| || ||||| ||||||||||| || || |||||||||||||||||||| ||||||||||| |||||||||||||||||   |||   | |  |  | |||   | |  | |  |  || ||    |  | |    | | ||      |    ||  |   |      ||         
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgtttgctt--atccgaccatcttatgtactagtcatctgtttttactgcccttatctgttgtctttcttcttggttgcacagttattttttagttttttgat

upper sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv13s0158g00360.t01 (Vitis vinifera), 5'ss of exon 4
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttggttctcctc-tgttactg-agttattaaatcattgtaaaatcgatgttctctatg-ttaaaaactcccgcgtat-acaacacacag----
| |   ||| || || ||||||||||| ||||| || || ||||||||||| ||||||||||| |||||||||||||||||||| ||||| ||||| |||||    ||     ||   | | | | || ||   ||   |      |  |||  | |||||     |||     |  |   ||| |||| | | |     
ATTTAAAGAAGTTGTGGCAGTGACTGGCGATGGGACCAACGATGCTCCTGCTTTGCATGAGGCGGACATTGGACTTGCCATGGGCATAGCAGGAACTGAGgtttgtttaataccttgccatataattgcagcagttctttggaatcatgatcatttttctcatcacttacccggtttcatttattacaagatagattcac

upper sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S37_351V6.1 (Physcomitrella patens), 5'ss of exon 6
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgta-gcctttggttctcctctg---ttactgagttattaaatcattg-taaaatcgatgttctctatgttaaaaactcccgcgtatacaacacacag---
| ||||||| || || || ||||| || ||||| || |||||||||||||| ||||||||  ||||||| ||| | || ||||| || || || ||||||||| |  |||  ||    ||||   | |   |||| |     ||| | ||   | |||   | |  |||| |   ||      ||        |  |   
ATTGGGAGAAGTGGTGGCCGTGACAGGTGATGGCACCAATGATGCTCCTGCTTTGCATGAATCTGACATCGGAATGGCGATGGGCATTGCGGGTACAGAGgtacgtatttttttacggtctgaagtgaaacagttgtggggccatggatagtcttgatcaacccgctgttcatgtctgtataataagtcgtcaatggcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|125273749|gb|EL287834.1|EL287834
EST:     GCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAG                         GTTGCGAAAGAGAATGCTGATGTTATCATAATGGACGACAACTTTGCAACA
genomic: GCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttg ... caacacacagGTTGCGAAAGAGAATGCTGATGTTATCATAATGGACGACAACTTTGCAACA
EST: gi|124974192|gb|EL047768.1|EL047768
EST:     CATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAG                         GTTGCGAAAGAGAATGCTGATGTTA
genomic: CATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttg ... caacacacagGTTGCGAAAGAGAATGCTGATGTTA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttggttctcctctgttactgagttattaaatcattgtaaaatcgatgttctctatgttaaaaactcccgcgtatacaacacacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA