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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAAGCTTCAGAACCCTACTCCACGTTTAAACGAGAGGATTCTCTCATCTTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCGgtaataatcactgttttaaagatattctgtgtgtttgattagagtctttttaactaaattgttctatgtgtgcag

Basic information

species Arabidopsis thaliana
transcript AT4G01480.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G01480.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os04g59040.3 (Oryza sativa), 5'ss of exon 2
AAGAAGCTTCAGAACCCTACTCCACGTTTAAACGAGAGGATTCTCTCATCTTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCGgtaataatcactgttttaaagatattctgtgtgtttgattagagt-ctttttaac-taaattgttctatgtgtgcag---------
     ||  |  |  |   | ||     | ||||||||||| || || || ||||| | |||||| || ||||||||||| |||||||||||||| |||||||   | |  | |||   |  | |  |    | |     | |   || | |  | |  ||  |   |  |     |         
GCTGGGCAGCCCAGGCGCGCCCCTAAGCTCAACGAGAGGATCCTGTCCTCCTTGTCGAGGAGATCAGTAGCTGCACATCCGTGGCATGATCTTGAGATCGgtatggaactgtctttcccatctctctttatggctcacccacaacactatgtggcatgcatcatctcacttaatttggttcaacag

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G061928_T04 (Zea mays), 5'ss of exon 2
AAGAAGCTTCAGAACCCTACTCCACGTTTAAACGAGAGGATTCTCTCATCTTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCGgta-ataatcac-----tgttttaaagatattctgtgtgtttgattagagtctttttaactaaattgttctatgtgtgcag
    |||  | |||     | ||     | || || ||||| ||||| ||| |||| | ||| || || ||||| |||||||||||||||||||| |||||||  |   |||     |  |||   | | ||||   |  ||  | | |      |  ||||| |  || |   | | |||
GCTGAGCAGCCGAAGAGGGCCCCTAAGCTCAATGAAAGGATCCTCTCTTCTCTGTCCAGGAGGTCCGTAGCTGCTCATCCATGGCATGATCTTGAGATCGgtacgttggcacaactatcctttcttgctcttctaactcctttgtcaaataagcatacactaattgattttggttatacag

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA07G05390.1 (Glycine max), 5'ss of exon 2
AAGAAGCTTCAGAA-----CCCTACTCCACGTTTAAACGAGAGGATTCTCTCATCTTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCGgtaat---aatcactgttttaaagatattctgtgtgtttgatta--gagtctttttaactaaattgttctatgtg--tgcag-----------------------------------------------------------------------------------------
      |||  |||      ||   ||| |||||||| || |||||||| ||||||||||||| |||||| |||||||| || || ||||||||||||||||| |||| |     ||||| ||||       |    | |  || |  |  || |   || ||  |  ||| | |||     ||  |                                                                                         
-----CCTTGCGAAAACCGTCCGGTTCCCCGTTTAAATGAAAGGATTCTTTCATCTTTGTCTAGGAGATCAGTTGCTGCTCACCCTTGGCATGATCTTGAAATTGgtactcttgttcacttttttgcttcattggcatttactttaacatcgaatgacttaaatcatgttgctatatccccttgtggctaggccaaatatgcttatgccaaaacaaggactagtttggtcttaccccacaaaaaaagttgttaatgttcttaggtttcatgtgcag

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA16G01960.1 (Glycine max), 5'ss of exon 1
----AAGAAGCTTCAGAACCCTACTCCACGTTTAAACGAGAGGATTCTCTCATCTTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCGgtaataatcactgtt--ttaaagatattctgtgtgtttgattagagtct-------ttttaactaaattgttctatg--tgtgcag-------------------------------------------------------------------------------------------
     ||||          ||   |||||| || || || |||||||| |||||| |||||| |||||| |||||||| || || ||||||||||||||||| ||||||  |   ||||   ||      |||  ||  ||| |||  |   |       ||  ||  || ||| | |||     ||  |                                                                                           
CCTCGAGAAAACC----GTCCGGTTCCACGCTTGAATGAAAGGATTCTTTCATCTCTGTCTAGGAGATCAGTTGCTGCTCACCCTTGGCATGATCTTGAAATTGgtaatc-ttgttgttgactacgttgcttcattgcatttaatttaacattgaatgacttaaaatcaagttgctatattatcttgtggctaggccaaatgcttatgctaaatcaaggattattttggtcttagcctacaaaaaaaaaaagttgttaatgttcttaggtttcatatgcag

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA03G42280.1 (Glycine max), 5'ss of exon 2
AAGAAGCTTCAGAACCCTACTCCACGTTTAAACGAGAGGATTCTCTCATCTTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCGgtaata--------atcactgttt---taaagatattctgtgtgtttgatt---agagtctttttaactaaattgttctatgtgtgcag
 ||||  |       ||   ||| ||||| ||||| || ||||| ||||||||||| || ||||| || ||||| ||||| ||||||||||||||||| |||| |         || | |||||   |    ||||  | |   |  ||||   | | | |||  ||   | ||  | |   | |||||
GAGAAAATC----GTCCAGTTCCCCGTTTGAACGAAAGAATTCTTTCATCTTTGTCAAAAAGATCAGTAGCTGCCCATCCTTGGCATGATCTTGAAATTGgtactgttgtcaatattattgtttatttgttcatatagtataattaagatttaaataatatttcaaaactacttaattttcatttgcag

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA18G18510.1 (Glycine max), 5'ss of exon 1
AAGAAGCTTCAGAACCCTACTCCACGTTTAAACGAGAGGATTCTCTCATCTTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCGgtaataatcactgttttaaagatattctgtgt-gtttgattagagtct---------ttttaactaaattgttctatgtgtgcag
| | ||    |    ||   ||    ||| || || |||||||| ||||| ||||| | |||||| || ||||| ||||| ||||||||||| ||||| |||||   |     | |||  | |  |   ||| || |  |||   | |         ||  ||   | ||  | |   | |||||
ATGGAGAAA-ACCGTCCAGTTCTCTATTTGAATGAAAGGATTCTTTCATCATTGTCAAGGAGATCAGTAGCTGCCCATCCTTGGCATGATCTAGAAATTGgtaactttgttgatattattgcttgttcatgtagtatagttaagatttaaatcatatttcaaaactacttaattttcatatgcag

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA19G45050.1 (Glycine max), 5'ss of exon 1
----AAGAAGCTTCAGAACCCTACTCCACGTTTAAACGAGAGGATTCTCTCATCTTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCGgtaataat-----cactgtt--ttaaagatattctgtgtgtttgattagagtcttttt---aactaaattgttctatgtgtgcag
     ||||  |       ||   ||| ||||| || || |||||||| ||||| ||||| | |||||| || ||||| ||||| ||||||||||| ||||| |||||   |      | | ||  ||    ||||  | |   |  ||||  | || | ||   ||   | ||  | |   | |||||
GCTGGAGAAAATC----GTCCAGTTCCCCGTTTGAATGAAAGGATTCTTTCATCATTGTCAAGGAGATCAGTAGCTGCTCATCCTTGGCATGATCTAGAAATTGgtaactttgctgatattattgcttgttcatatagtatagttaagatttaaatcatattacaaaactacttaattttcatatgcag

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 5'ss of exon 1
-AAGAAGCTTCAGAACCCTACTCCACGTTTAAACGAGAGGATTCTCTCATCTTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCGgta-------ataatcactgttttaaagat---attctgtgtgtttgattagagtctt----tttaactaaattgttctatgtgtgcag
 | || |||||| ||| |   ||| |  || || |||||||| ||||||||  |||| | ||||||||||||||| ||||| |||||||||||||| || |||        | |||   | | || |   |   | |    |  |    || ||  ||     |||   || |   || ||| | |||||
TACGATGCTTCACAACGCCCATCCTC-CTTGAATGAGAGGATCCTCTCATCAATGTCAAGGAGATCGGTTGCTGCTCATCCCTGGCATGATCTTGAGATTGgtgtgtctcgagaatggttatgttcatagttcaaattgcagcctccatttggaaactaacggtttttgtatacc-ttgtatatatgcag

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S552_1V6.1 (Physcomitrella patens), 5'ss of exon 2
---AAGAAGCTTCAGAACCCTACTCCACGTTTAAACGAGAGGATTCTCTCATCTTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCGgtaataatcactgttttaaagatattctgtgtgtttgattagagtctttttaact-------aaattgttctatgtgtgcag-------------------------------------------------------------------------------------
   |      |||| ||  |||||||||   | |||    ||||| |  |  |  ||       |  | || ||||||||||||||||||||||| ||||||||||        |||    |    ||| |  ||   |  |   | |       | |       | | |||  || ||||  |                                                                                      
TCAACTGCAGTTCACAAGGCTACTCCAC---TGAACAGCCGGATTATGACGACGATGGAGCGTCGTACTGTCGCTGCACATCCATGGCATGATCTCGAAATCGgtatgtgggtttgtaccgacaggatttttggttagttgtggaaatggccgcgagtcgggaagagagtgtcataggtgtttatcgtgcattgcttatcgttgtaggtgtagtggaagtatctgaatgatgaggttctgaattggtgtgtgttgtattgcctttttcag

upper sequence: AT4G01480.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 3
AAGAAGCTTCAGAACCCTACTC--CACGTTTAAACGAGAGGATTCTCTCATCTTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCGgtaataatcactgttttaa-agatat-tctgtgtgtttgattagagtctttttaactaaattgttcta--tgtgtgcag---------------------
   |  || | |  |   |  |  |||   | ||| |  | ||| | ||| |  ||  |    ||||||||||||||||||| ||||||||||||||||| |||    ||| |  | | || |||| | | | | | |||  |||   |  |||| | |   || || |   | | ||                        
--AATTCTGCGGTTCATCAACCAGCACCACTCAACCACCGCATTTTGTCAACAATGGATCGACGATCGGTTGCTGCACATCCGTGGCATGATCTTGAAATTGgtgtggatctccttgtcaatagatctatttctttatttctttatttttatttttatttctttatttttattttttgtgatctttgtgttcataagaagtt

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|116470399|gb|EG512991.1|EG512991
EST:     TTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCG                         GACCTGGAGCTCCAGTGATTTTCAATGTG
genomic: TTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCGgtaataatca ... atgtgtgcagGACCTGGAGCTCCAGTGATTTTCAATGTG
EST: gi|116470397|gb|EG512989.1|EG512989
EST:     TTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCG                         GACCTGGAGCTCCAGTGATTTTCAATGTG
genomic: TTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCGgtaataatca ... atgtgtgcagGACCTGGAGCTCCAGTGATTTTCAATGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAAGCTTCAGAACCCTACTCCACGTTTAAACGAGAGGATTCTCTCATCTTTGTCTAAGAGATCGGTTGCTGCACATCCATGGCATGATCTTGAAATCGgtaataatcactgttttaaagatattctgtgtgtttgattagagtctttttaactaaattgttctatgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC