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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttccattgcctgatatatagctttttgtttacaaactgttaatgttagaagttcgaagtagtttcaactaaaacctataatgacattgtatgtttgtggttcag

Basic information

species Arabidopsis thaliana
transcript AT2G27860.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 6
TCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttccattgcctgatatatagctttttgtttacaaactgttaatgttagaagttcgaagtagtttcaactaaaacctataatgacattgtatgtttgtggttcag
||| || ||||| ||||| || || ||||| ||||||||  | || ||||||||||| || ||||| || ||||| ||||||||||| |  |||||||||||| |||   |    | || | ||  |  ||   |         | ||| ||||  | |   ||   || |||| |||  | ||       | |||||     |     
TCTCCTGCGTCGGGAGCCCCTGAAACTTGTTGATGGTGGCCAGTCCCAGAGAACTTTTGTTTACATTAAGGATGCCATTGAAGCTGTTCACTTGATGATTgtatgttttctctgtttatctttacttcctttgct--------cttatgctagatttaccttgttagttgaactgaaatgtgta------ctttatgtcaaaag-----

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G063949_T01 (Zea mays), 5'ss of exon 6
TCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttccattgcctgatatatagctttttgtttacaaactgttaatgttagaagttcgaagtagtttcaactaaaacctataatgacattgtatgtttgtggttcag
||| || ||  | |||||  | |||||||| ||||| ||  | || |||||||| || ||||||||||| |||||||| ||||||||  |  ||||||||||| ||| |   |  | || | | |||  ||||||  |  |   ||||   |  ||   ||| |  | |   | |   |  |                           
TCTGCTCCGGAGAGAGCCCTTGAAGCTTGTTGATGGGGGTCAGTCTCAGAGAACCTTTGTCTACATCAAGGATGCTATCGAAGCTGTAGTGCTGATGATTgtatgttgctgcgttt-atctctggctccttgtttttatgc-actaatccaatgaggctgaactcttgttgtcaattgcaaaag-------------------------

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA12G30490.1 (Glycine max), 5'ss of exon 6
TCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttccattgcctgat------atatagctttttgtttacaaactgttaatgttagaagttcg------aagta--gtttcaactaaaacctataatgacat-tgtatgtttgtggttcag--
||| || ||| | ||||| ||||||||||| ||||||||  |||| ||||| ||||| || || || || |||||||||||||||||| | |||||||||||| |||||  |  |  ||      ||  | |||| | | |   || |  | ||  ||||| |||       || ||   ||     |  |   |  ||  | || || | | |  |  || |   
TCTCCTCCGTGGAGAGCCCCTCAAGCTTGTGGATGGTGGCCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCTGTCTTATTGATGATTgtaggttcccatatccaatctttttatgcaactttatatattttaagttctgattgtagaatttcatctttaaactattattcttgttggatggttcaactaaatgtgaacgataatttttaacag

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA11G19550.2 (Glycine max), 5'ss of exon 6
TCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttccattgcctgatatatagctttttgtttacaaactgttaatgttagaagttcgaagtagtttca-actaaaacctataatgacattgtatgtttgtggttcag
|||||| ||  | ||||| ||||||||||| || |||||  | || |||||||| ||| | ||||| || |||||||||||||||||| | ||||||||||||||||| | || |  || | ||  ||||||       ||||||  ||||  || | |  | |  | | | | |    | | |      ||||| ||||    | |   
TCTTCTCCGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttctaatgtcctatcttta--tttttg-----ggactgtttgtgttttaaatacagattcatgtgatattttttcatgttcaattattgt-tgttgtcagctg--

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 6
TCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttccattgcctgatatatagctttttgtttacaaactgttaatgttagaagttcgaagtagtttcaactaaaaccta--taatgacattgtatgtttgtg-gttcag-------------------
|||||| ||  | ||||| ||||||||||| || |||||  | || |||||||| ||| | ||||| || |||||||||||||||||| | ||||||||||||||||| | || |  || | ||  |||  |  |      ||||     || |  ||| | ||  | |    | |     |  || ||   ||||  | | ||    | ||                   
TCTTCTCCGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTCATTTACATTAAAGATGCTATTGAAGCTGTCTTGTTGATGATTgtacgttctaatgtcctatctttatttttgggactgtttg-tgttttaaatacagattc-atgtgatattttttcatgttcaattattgttgttgtcagctggtccactgagtgttatgacctgttaacag

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA17G05440.1 (Glycine max), 5'ss of exon 4
TCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttccattgcctga-tatatagctttt---tgttta-caaactgttaatgttagaagttcga--agtagtttcaactaaaacctataatgacattgtatgtttgtggttcag--
||| || ||  | ||||| ||||||||||| ||||||||  |||| ||||| ||||| || || || || |||||||||||||| ||| | |||||||||||| |||||  |     | | ||||  ||||   |  | | |  | |||  | |||     || ||  | || | |    | |    |  | | |   || | | |  |  || |   
TCTCCTCCGCGGAGAGCCCCTCAAGCTTGTGGATGGTGGTCAATCCCAGAGGACTTTTGTGTATATTAAGGATGCTATTGAAGCCGTCTTATTGATGATTgtaggttcccatatgaaactttatatattttaagtactgatctgattgtagaagttcatcttttgactattattcttgtttcatggttcaactaaatgtgaacgataatttttaacag

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA12G08930.1 (Glycine max), 5'ss of exon 6
TCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttccattgcctgatatatagctttttgtttacaaactgtt--aatgttaga-agttcgaagtagtttcaactaaaacctataatgacattgtatgtt----tgtggttcag-------------
||||||  |  | ||||| ||||||||||| || |||||  | || |||||||| || || ||||| || |||||||||||||||||| |  |||||||||||||||| | || || || | ||  |||  |  |      | ||  |||   | | || || | ||  |||    |  ||   | | |    |||  || |    || |  | |              
TCTTCTCAGAGGAGAGCCCCTCAAGCTTGTGGACGGTGGCCAGTCCCAGAGAACCTTTGTTTACATTAAAGATGCTATTGAAGCTGTCTTGCTGATGATTgtacgttctaatgtct-atctttatttttgggactgtttgttttttaaataccatacaggtccatgtgatttttttttcaagtcaaattattgttggctggtccactgagtgttatgacctgttaacag

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 6
TCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttccattgcctgatatatagctttttgtttacaaactgttaatgttagaagttcgaagtagtttcaactaaaacctataatgacattgtatgtttgtggttcag
 ||||| ||||||||||| ||||||||||| ||||||||  |||| |||||||| || || || || || |||||||||||||| ||| | |||||||||||  |||  |    |   | | |   | | || || || |   ||| | |    | || |||  |     |||   |  ||  |||   ||  | | ||    |     
CCTTCTTCGTCGTGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTATATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgtgagttg-accatcctttctttcattatatgattccacat--ttagttt----acttggaaaaaaaaaaaacaggatgctg-aatattatgatcttttctcag-----

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 6
TCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttccattgcctgatatatagctttttgtttacaaactgttaatgttagaagttcgaagtagtttcaactaaaacctataatgacattgtatgtttgtggttcag
 ||||| |||| |||||| ||||||||||| ||||||||  |||| |||||||| || || ||||| || |||||||||||||| ||| | |||||||||||    |  |    |     | |   | | || || || | |     |  | | |     ||   |||    || ||  |||| ||    |   |              
CCTTCTTCGTCATGAGCCACTCAAGCTTGTGGATGGTGGCCAATCCCAGAGAACCTTTGTTTACATAAAGGATGCTATTGAAGCAGTCTTGTTGATGATTgt-tagtggaccatccttcctttcattatctgattccacatttagcttacttggaaaaaaaaaaggtt---gctgaatactatgatattttctcag-------------

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ18978 (Selaginella moellendorffii), 5'ss of exon 6
TCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttccattgcctgatatatagctttttgtttacaaactgttaatgttagaagttcgaagtagtttcaactaaaacctataatgacattgtatgtttgtggttcag
  | ||     | |||||||| ||||| || ||||||||| |||||||  | || |||||||||||||| ||||| ||||| || ||  |    ||| | ||| |   |  ||        |||  |       |  |  ||  | |  || |||    ||                                                
CTTGCTCAAGAGCGAGCCTCTAAAGCTCGTCGATGGTGGACAATCACAACGGACGTTCGTCTACATCAAGGATGCCATTGACGCGGTGATGCGTATGGTGgtaagcctctatgatgttggaataaatc--cagatgtagtctaatcac-ttggaaccatgacag---------------------------------------------

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: EFJ07025 (Selaginella moellendorffii), 5'ss of exon 6
TCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttccattgcctgatatatagctttttgtttacaaactgttaatgttagaagttcgaagtagtttcaactaaaacctataatgacattgtatgtttgtggttcag
  | ||     | |||||||| ||||| || ||||||||| |||||||  | || |||||||||||||| ||||| ||||| || ||  |    ||| | ||| ||  |  ||        |||  |       |  |  ||  | |  || |||    ||                                                
CTTGCTCAAGAGCGAGCCTCTGAAGCTCGTCGATGGTGGACAATCACAACGGACGTTCGTCTACATCAAGGATGCCATTGACGCGGTGATGCGTATGGTGgtaagtctctgtgatgttggaataaatc--cagatgtagtctaatcac-ttggaaccatgacag---------------------------------------------

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|124946857|gb|EL022740.1|EL022740
EST:     ATGATGCTATTGAAGCTGTCCTTTTTGATGATT                         G-AAACCCAGAGAGGGCAAATGGGCACATCTTCAACGTAGGCAACCCGAAC
genomic: ATGATGCTATTGAAGCTGTCC-TTTTGATGATTgtacgttcca ... tgtggttcagGAAAACCCAGAGAGGGCAAATGGGCACATCTTCAACGTAGGCAACCCGAAC
EST: gi|116422972|gb|EG465564.1|EG465564
EST:     GAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATT                         GAAAACCCAGAGAGGGCAAATGGGCACATCTTCAACGTAGGCAACCCGAAC
genomic: GAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttcca ... tgtggttcagGAAAACCCAGAGAGGGCAAATGGGCACATCTTCAACGTAGGCAACCCGAAC
EST: gi|124786829|gb|EH876508.1|EH876508
EST:     CCTTTTGATGATT                         GAAAACCCAGAGAGGGCAAATGGGCACATCTTCAACGTAGGCAACCCGAAC
genomic: CCTTTTGATGATTgtacgttcca ... tgtggttcagGAAAACCCAGAGAGGGCAAATGGGCACATCTTCAACGTAGGCAACCCGAAC
EST: gi|116380174|gb|EG422766.1|EG422766
EST:     GAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATT                         GAAAACCCAGAGAGGGCAAATGGGCACATCTTCAACGTAGGCAACCCGAAC
genomic: GAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttcca ... tgtggttcagGAAAACCCAGAGAGGGCAAATGGGCACATCTTCAACGTAGGCAACCCGAAC
EST: gi|125273593|gb|EL287678.1|EL287678
EST:     AACTTTCGTCTACTATCAATGATGCTATTGAAGCTGTCCTTTTGATGATT                         GAAAACCCAGAGAGGGCAAATGGGCACAT
genomic: AACTTTCGTCTAC-ATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttcca ... tgtggttcagGAAAACCCAGAGAGGGCAAATGGGCACAT
EST: gi|125142397|gb|EL179719.1|EL179719
EST:     ATGATGCTATTGAAGCTGTCCTTTTTGATGATT                         GAAAACCCAGAGAGGGCAAATGGGCACATCTTCAACGTAGGCAACCCGAAC
genomic: ATGATGCTATTGAAGCTGTCC-TTTTGATGATTgtacgttcca ... tgtggttcagGAAAACCCAGAGAGGGCAAATGGGCACATCTTCAACGTAGGCAACCCGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTCTACGTCGTGAGCCTCTCAAGCTTGTAGATGGTGGAGAATCACAGAGAACTTTCGTCTACATCAATGATGCTATTGAAGCTGTCCTTTTGATGATTgtacgttccattgcctgatatatagctttttgtttacaaactgttaatgttagaagttcgaagtagtttcaactaaaacctataatgacattgtatgtttgtggttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG