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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagagacttagagttttgcctttgtttttaatgatccgtttggaatttataaacttacttttgttgttttcttcgccagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG

Basic information

species Arabidopsis thaliana
transcript AT2G29080.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g38400.2 (Oryza sativa), 3'ss of exon 5
---------------------------------------------------------------------------------------gttagagacttagagttttgcctttgtttttaatgatccgtttggaatttataaacttacttttgt----------tgttttcttcg-ccagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG
                                                                                       |||  |    |  | |  |||  | | |  |  | |  ||||   || ||| ||    |  | | |          | || | || | |||| | | ||| |||||||| ||||| ||||| || ||||| |||||||| ||||||||||| |||||||||||||| || |||||||||||||| || || |
gttagttcattctcttcttctgttctactttgaaacgactgtcaaatatgaaatatatacatgcacattgattctcaagctctgctagttccacctattcaataatgcagtagctactgcttaaacgttgttaagttacaataaaaactgtataatgacaagcttttctgttggtccagGTGTTTTTTAAGGATGTAGCTGGTTGTGATGAAGCTAAGCAAGAAATAATGGAGTTTGTGCATTTCCTTAAGAATCCCAAGAAGTATGAAGAGTTAGGAG

upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g62500.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------------gttagagacttagagtt--ttgcctttgtt--------tttaatgatccgtttg---gaattta-taaacttacttttgttgttttcttcgccagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG
                                                                          ||| |     |||  ||  |  || |||          |  ||| |    ||      | | || | || | || ||  || || | | |  ||| | |  || |||||||| ||||| ||||| || || ||||||||||||||||| ||||| |||||||| || || || ||||| ||||||||  |||| |
gttagtttttatttgctatttccatctcttgctattttgaacaaaacatgaaattcatatccttttttgtaaatgtttgttctgtagctttattcaccattgacaaagaacatacaataacatattcatataattctactgaagtaaccttgtttcttgtgtgctacagGTGTTCTTTAAGGATGTAGCTGGCTGTGATGAAGCCAAACAAGAAATTATGGAATTTGTTCATTTCCTGAAAAATCCCAAGAAATATGAAGAACTGGGAG

upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G038401_T01 (Zea mays), 3'ss of exon 5
--gttagagacttagagttttgcctttgtttttaatgat--------ccgtttggaatttataaacttactttt-----gttgttttcttcgc--------cagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG
  |||  ||  | |    |||||| || | || |   |         |    || ||||   | | ||   |||       ||| | |||  |        ||| | | ||| |||||||| || || |||||||| || ||||||||||| ||||||||||| ||||||||||| ||||| |||||||||||||||||||| |
ttgttgtagcttca----tttgcccttttcttaagaaacaaagcatactacatgaaattcgaagatttgtcttttcatcaatgtctacttttctgctggtccagGTGTTTTTTAAGGATGTAGCCGGTTGTGACGAAGCAAAACAAGAAATAATGGAGTTTGTGCATTTCCTTAAAAACCCTAAGAAGTATGAAGATTTGGGAG

upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------------------------------------------------gttagagacttagagttttgcctttgtttt--taatga-tccgttt---ggaatttataaacttacttttgttgttt--tcttcgccagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG
                                                                                                               |  || |        | |    |   ||   ||| | | | |||    ||   |||  |  | ||| | ||||||  | ||   ||||| ||||| || ||||||||||| ||||| ||||| || |||||||||||||||||||| || ||||| |||||||||||||| ||||||||  | ||||
gttgggagatttctttttcttctaccaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttcttgttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTTGGTG

upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G14640.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------------------------------------gttagagactt------agagttttgcc---tttgtttttaatga-tccgtttggaattta----taaacttacttttgttgttt--tcttcgccagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG
                                                                                                      ||||    ||        ||||  |||    |   ||   ||| | | | |||   |   |    | | |||  |||| ||||||  | ||   ||| | ||||| || ||||||||||| ||||| ||||| || |||||||||||||||||||| || ||||| |||||||||||||| ||||||||  | ||||
gttaggagatttctttttcttctatcaatgagatggctgctgttttttgtgtttgttttaatagcgtgttccccacttgctgttgttatctttccagttttggttatttcctcctggcaggagtgctgctaaataacttgacaataagttcatttaagagacaatatttatcttcttttttttgtttcattttgttcagGTCTATTTTAAAGATGTTGCTGGTTGTGATGAGGCGAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAACCCAAAGAAATATGAAGAACTCGGTG

upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G06580.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------------------------------------------------------gttagagacttagagttttgcctttgtttt--taatga-tccgttt---ggaatttataaacttacttttgttgttt--tcttcgccagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG
                                                                                                               |  || |        | |    |   ||   ||| | | | |||    ||   |||  |  | ||||| ||||||  | ||   ||||| ||||| || ||||||||||| ||||| ||||| || |||||||||||||||||||| || ||||| |||| ||||||||| ||||||||  | ||||
gttgggagatttctttttcttctatcaatgagatggctgctgatgtttgtgtttgttttaatagcatgttccccatttgccattgttatctttccagttttagttatttcctccaggcaggagtgctggtaaataacttgacaataagttcatttaagagacaatatttatcttctttttttgtttcattttgttcagATCTATTTTAAAGATGTTGCTGGCTGTGATGAGGCAAAGCAAGAAATTATGGAGTTTGTCCACTTCCTCAAGAGCCCAAAGAAATATGAAGAACTTGGTG

upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0007g00560.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------------------gttagagacttagagttttgcctttgtttttaa--tgatccgtttggaatttataaacttacttttgttgttttcttcg-----ccagATTTATTTCAAGGATGTTGCTGGATG----TGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG---------------
                                         ||   | ||  ||     |   | || || ||  | |    ||  | |   ||||  || ||||||   |||| |  |     |||| | |||||||||||||| ||||| ||    ||| ||||| || |||||||| ||||||||||| || ||||| ||||| |||||||| ||||| || ||||| |               
gtcagccatggcatttcatttacttcagattatctcacagattttggtctatgaagaaagaaatggtattcaaactaagttcttcagcaaggataa--ttgcttttgaatttttatgtggcaatccaggtatatttcaaggatgtagCTGGCTGGCTGTGATGAGGCAAAGCAAGAAATCATGGAGTTTGTGCACTTCCTCAAGAAGCCAAAGAAATATGAGGAGTTGGGAGCAAAAATTCCAAAAG

upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------------------------------------------------------gttagagacttagagttttgcctttgtttttaatgatccgtttggaatttataaacttacttttgttgtttt----cttcgc-cagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG
                                                                                                        |||| |  | |    ||||  || | |   || |  |    ||   |||  ||   ||  |||   | ||||    | | |  ||| | | |||||| ||||||||||||||||| || || || |||||||| ||||| ||||| || ||||| ||||| || || || |||||||| ||||| |
gttagctaactgtttcttttgtcaaaggtggtttgtctttagtttgcagcatccaatatttttacagtatacaataattattatatcctccttgctcacctatggttataatcattcgattttctctctctgactattattattattatcattattattgtttgtttatctatttttggacctagtacagGTCTTTTTCAAAGATGTTGCTGGATGTGATGAAGCAAAGCAAGAAATCATGGAATTTGTTCACTTCCTCAAGAATCCTAAAAAATATGAAGAGTTGGGAG

upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S346_22V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------gttagagacttagagttttgcctttgtttttaatgatccgtttggaatttataaacttacttt-tgttgttttcttcgc-cagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG
                  |        | |   | | | |||| |      | | | ||||   |||  |||     | | | || |||  | | | ||| |    ||||| ||||||||||| ||||||||||| |||||||| ||||||||||| || || ||  | || ||||| ||||||||| | ||  | ||||
aagttataagtgggaacatgtcgcgtatggccatgtacatttggtacagtagttgcatttgtctttttgaaaagaggtgtattttatttgatcctcacagGTAATGTTCAAAGATGTTGCTGGTTGTGACGAGGCAAAACAAGAGATTATGGAGTTCGTTCACTTTTTGAAAAACCCCAAGAAGTATCAGGAACTTGGTG

upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S456_6V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------gttagagacttagagttttgcctttgtttttaatgatc-cgtttggaatttataaacttacttttgttgttttcttcgc-------cagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG
           | |      | |  ||      ||||    ||||||   |||        || |   ||  ||||| ||| |   | |        ||| ||   ||||| |||||||| || ||||||||||| |||||||| ||||||||||| || || ||  | |||||||| ||||||||  ||||  | ||||
ggatgagagatgctgttccatgatggtgagctatttgccaataatgaagacgtactaggggtagagttttgtttttgatgtatctgttgtgtcattacagGTTATGTTCAAAGATGTTGCCGGTTGTGACGAGGCAAAACAAGAGATTATGGAGTTCGTTCACTTTTTGAAGAACCCCAAGAAGTACCAAGAACTTGGTG

upper sequence: AT2G29080.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S39_149V6.1 (Physcomitrella patens), 3'ss of exon 5
gttagagacttagagttttgcctttgtttttaatgatccgtttggaatttataaacttacttttgttgttttcttcgc--cagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG
                       |  | | | ||||  |      |||     | |||  ||||||   ||   | ||  ||| |    ||||| ||||||||||| || |||||||| |||||||| || ||||| ||||| || ||| | ||||| || ||||| ||| ||||  | || |
----------------------gtgatgtcttatgactcccggaaaatgacggagctttattttgtgcgttgtgttgctgcagGTGATGTTCAAAGATGTTGCTGGTTGCGACGAGGCAAAACAAGAGATCATGGAATTTGTTCACTTCTTGAAGAATCCCAAGAAATATCAAGAACTTGGGG

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|116477683|gb|EG520275.1|EG520275
EST:     ATATAGGCAAAGCTACAATAACGAGAGCTGATAAACATTCCAAGAATAAG                         ATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATG
genomic: ATATAGGCAAAGCTACAATAACGAGAGCTGATAAACATTCCAAGAATAAGgttagagact ... tcttcgccagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttaatgatccgtttggaatttataaacttacttttgttgttttcttcgccagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG
                           aacttac  putative branch site (score: 2)
                             cttacttttgttgttt  CT-rich tract
                   aatttataaacttact  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagagacttagagttttgcctttgtttttaatgatccgtttggaatttataaacttacttttgttgttttcttcgccagATTTATTTCAAGGATGTTGCTGGATGTGACGAGGCTAAACAAGAAATTATGGAGTTTGTACATTTCCTTAAGAACCCAAAGAAGTATGAAGATTTGGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA