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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtttaatctcccattcacattttctttttctctctgataaaatcaagtcatttgttcttataatttgatttctctgtcag

Basic information

species Arabidopsis thaliana
transcript AT1G72730.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G20300.2 (Glycine max), 5'ss of exon 4
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtttaatctcccattcacattttctttttctct---ctgataaaatca-agtcatttgttct-tataatttgatttctctgtcag--------
 |||||| || | || || || || || ||  | |||   || || ||||||||| | ||||| |||||||||||||| || ||||||||||||||||||||||    ||||||    |      ||||||||| | ||   |   || ||  | ||   ||  | ||| || ||    |||| |   ||             
GTTTGACATGCTGCGGAGGCAGTCTCTTCGCCCAGATTGCATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAGgtttg---ttgttttgattagttcccacattttcatatttagtgcactaatttattcttggttgtctgtcctatacttgttgactatcctacttcttgtgttg

upper sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA13G42360.1 (Glycine max), 5'ss of exon 4
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtttaatctcccattc--acatt---ttctttttctctctgataaaatcaagtcatt-tgttcttataatttgatttct-ctgtcag---
 |||||| || |||| ||||| || || ||| | |||   || || ||||||||| | ||||| |||||||||||||| ||||||||||||||||| ||||||| ||  | ||  || |    ||   |||||   || ||||| | |||  | |   |      |  | |     |  ||| ||   |  |  ||    
ATTTGACATGCTACGGAGACAGTCTCTTCGTCCAGATCACATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAGgtttgatggttttccatgtttgtttaaaacattgaattgtttttttttcttctgattcctgactgtcatctaaacgttctttcatgcatgttaccaatat

upper sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA15G03020.1 (Glycine max), 5'ss of exon 4
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtttaatctcccattcaca---------ttttctttttctctctga-taaaatcaagtcatttgttcttataatttga----tttctctgtcag-----------------------------------------------------------------------------
 |||||| || |||| |||||||| || ||  | |||   || |||||||||||| | ||||| |||||||||||||| || |||||||||||||| ||||||| ||  | ||  || |    |  | |         | || || || ||  ||| |   ||| |  ||||  ||| |  |  ||||     |||| | |                                                                                
GTTTGACATGCTACGAAGACAATCTCTTCGCCCAGATCACATAAAAATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGACCAGgtttgatggttttccatgttttgtctaaaactttgaattgtttttcttttccttgagtgtcatctaaacattctttcatgcatgttgaaataattctttatttaaaacctgtgtgctagatgaagtcatcttgtgttagatagatagctaacagtttatatttttcgtgcatgaaatgcag

upper sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA07G00950.1 (Glycine max), 5'ss of exon 4
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtttaatctcccattcacattttctttttctctctgataaaatca-agtcatttgttct-tataatttgatttctctgtcag------------
 |||||| || | || || || || || ||  | |||   || || ||||||||| | ||||| |||||||||||||| || |||||||| |||||||||||||  | || || | |  |   ||  ||| ||   |    | || ||  |  |   ||  | ||| || ||    |||| |   || ||              
GTTTGACATGCTGCGGAGGCAGTCTCTTCGCCCAGATTGCATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAGgtttgttatt-ttgattaccatgttttcatatttagtg---cactaatttatccttggttgtctgtcctatacttgttgactatcctatctcttatgttggtaa

upper sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA17G06110.1 (Glycine max), 5'ss of exon 4
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtttaatctcccattcacattttctttttctctctgataaaatcaagtcatttgttcttataatt--tgatttctctgtcag------------
 |||||  || | ||| |||| || || |   | ||    ||||| ||||||||  | ||||| |||||||||||||| || || |||||||||||||||||   | ||| || |||   | | |||  |  |  ||||| || | || |   | | |  ||| |  || | ||   | ||  ||      |            
GTTTGATATGCTGCGCCGACAGTCACTTCAGCCAGACCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTCAAGGATCAGgt---acctt-ttcaattcacaactcatttagtacttttcactttaattattactaatactttatgtttttgataagtaatgcctacacttgtctatggatttt

upper sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA04G05580.1 (Glycine max), 5'ss of exon 4
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtt-------taatctcccattcacattttctttttctctctgataaaatcaagtc--atttgttcttataatttgatttctctgtcag-
 |||||| || | ||||| |||||  | ||  |||||   ||||  ||||||||  | ||||| || ||||| ||||||||||| |||||||||||||||||    || | ||       |  ||||   |      ||  || |  | | || |    |  | |   ||||   |||| || |    ||   |||    
ATTTGACATGCTGCGCAGGCAATCATTGCGCTCTGATAACATCAGGATGTTTGTATTGGATGAGGCAGATGAGATGCTCTCTCGAGGTTTCAAGGATCAGgtcctctcattttcccatgttgctctcttttatttgcttcattctattgtttgttgtgttggaatacgattttggcttaaaaataatatttagtgttttt

upper sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA06G05580.1 (Glycine max), 5'ss of exon 4
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtt---taatcttgtttaatctcccattcacattttctttttctctctgataaaatcaagtcatttgttcttataatttgatttctctgtcag-------
 |||||| || |  ||||||||||  | ||  |||||   ||||  ||||||||  | ||||| || ||||| ||||||||||| |||||||||||||||||    | || ||  |      | |  |   |||  |||  |     || |         |   ||     ||  ||||  ||| |   |          
ATTTGACATGCTGTGCAGACAATCTTTGCGCCCTGATAACATCAGGATGTTTGTATTGGATGAGGCAGATGAGATGCTCTCTCGAGGTTTCAAGGATCAGgtcctctcattttcctatgctgctctcttttattggcttcattctattgtttgtggattttggcttaaaaatactatttagttttttatttgaattttca

upper sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA15G18760.3 (Glycine max), 5'ss of exon 4
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgttt------aatcttgtttaatctcccattcacattttctt-------tttctctctgataaaat--caagtcatttgttcttataatttgatttctctgtcag
 |||||  || | |||||||| || || ||  | ||    ||||| ||||||||  | ||||| |||||||||||||| || |||||||| || |||||||||       |||| | ||   | |   | | |    ||  |       |||||   | || | ||   | | |    |||  | || |||  |   |       
ATTTGATATGCTGCGCAGACAGTCACTTCGGCCAGACTACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGTGGTTTTAAAGATCAGgttctttctaaatcatattccttttgttaatgaagaattactgattggatttcttgtttatgatatgtaatgccccacgtttctgtatttttgtacattg-----

upper sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA09G07530.3 (Glycine max), 5'ss of exon 4
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtttaatctcccattcacattttctttttctctctgataaaatcaagtcatttgttcttataatttg---atttctctgtcag---------
 |||||  || | |||||||| || || ||  | ||    ||||| ||||||||  | ||||| |||||||||||||| || |||||||| || ||||||||    | |  || |   ||   ||   | |||  | |  |  ||||    |     |  |||     | ||||      |  | |||||            
ATTTGATATGCTGCGCAGACAGTCACTTCGGCCAGACTATATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGTGGTTTTAAAGATCAGgtgctttttaattcatattctttttgttaattt--tataattactgactggacttgttgtttttgatatgtaatgcccacacgtttctgtatttttgtacat

upper sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA13G16570.1 (Glycine max), 5'ss of exon 4
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtttaatctcccattcacattttctttttctctctgataaaatcaagtcatttgttcttataattt----gatttctctgtcag------
 |||||  || | |||||||| || || |   | |||   ||||| ||||||||  | ||||| |||||||||||||| || || ||||| |||||||||||    |    ||||||      |  |  ||||  || | | |   |   |||     || ||||      | |||     |||  | ||| |       
GTTTGATATGCTGCGCAGACAGTCACTTCTGCCAGATCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttcactttaattattactaaatttttttgttgttttttacaagtaatacctacacttgtctacggatttttttaaattgatgtgtaaacgttcg

upper sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv04s0008g01000.t01 (Vitis vinifera), 5'ss of exon 3
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtttaatctcccattcacattttcttttt-ctctctgataaaatcaagt-catttgttcttataatttgatt---tctctgtcag-----
 |||||| |||| ||||| ||||| || ||| |||||   || || ||||||||  | |||||||| ||||||||||| || || |||||||||||||||||     |||      |   |  |  |  ||||  || | || | || ||  |     |  |  |||   ||| || |  |    | | |||| |     
TTTTGACATGTTGCGCAGGCAATCACTTCGTCCTGATTACATTAAGATGTTTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtccttcctttgcctttgctctgtatatctttttgttgtgctgtttgctactactctctataactgtcagtatgatgttgtcagatttttgtctggatat

upper sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv11s0016g01920.t01 (Vitis vinifera), 5'ss of exon 3
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtttaatctcccattcacattttctttttctctctgataaaatcaagtcatttgttcttataatttgatttctctgtcag------------
 |||||| || | || ||||| ||||| ||| |||||   || |||||||||||  | |||||||| ||||||||||||||||| |||||||||||||||||      |           ||||||  ||| | ||    | | ||  |||||     |||    |   ||| | |  |  |  | | ||            
ATTTGACATGCTGCGAAGACAGTCCCTTCGTCCTGATTACATTAAAATGTTTGTGTTGGATGAAGCAGATGAAATGCTCTCTCGAGGTTTCAAGGATCAGgtcattcttaaaccctaaatccattcttattgttttcacttttgtggcaaaattt--ccatcaactgcaatattcttttgacagtatgagtatatgatgcat

upper sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv09s0002g01760.t01 (Vitis vinifera), 5'ss of exon 4
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatct----------tgtttaatctcccattc--acattttctttttctctctgataaa----atcaagtcatttgttcttataatttgat-ttctctgtcag-----------------------------------------------------------------------------------
 |||||| |||| || ||||| || || ||  | |||   || || ||||||||  | ||||| |||||||||||||| || || ||||||||||||||||| |  |||          |||||  |  |   ||   | |||||    | ||   || | ||    || |  |   |  || ||| || || ||  ||  ||                                                                                       
GTTTGACATGTTGCGGAGACAGTCACTTCGCCCAGATTACATTAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtctgttctattatatctctgtttctttactagttgtaatatttttgcatacttcatggtgaagaacattattttgctaattgttagaagttcatgctcattgcttattgctggatttttcaatatgtgcaagttttgactggctttgttgtttttctgataattcattaattttttttgctgctgtcag

upper sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv04s0008g00980.t01 (Vitis vinifera), 5'ss of exon 1
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtttaatctcccattcacattttctttttctctctgataaaatcaagtcatttgttcttataatttgatttctctgtcag
      |  | |  |  |    || |||| ||||||  | ||||| ||||||||||| ||||| |||||||||||||||||| | || || ||||||||||| |    || | ||  |||   | |   ||||| |      | |  ||    |||  | | ||||| || | | |  | |  |   |||
------CACGCTGAGGCGGGGCTCTCTCCATGCTGACTCCATCAAGATGTTTGTTCTGGATGAGGCTGATGAAATGCTCTCTAGAGGCTTTAAGGATCAGgtct----ttatctag-ctcttgtccgtgttttcataagaatttttgta--gccaaaacttgtgttcctaaattgttttcttgcctgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtttaatctcccattcacattttctttttctctctgataaaatcaagtcatttgttcttataatttgatttctctgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT