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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcatctggtcatttaccggttattaagtatgtttgtcgagtatgtttttatcgaaattctctactggttttggcagGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT

Basic information

species Arabidopsis thaliana
transcript AT2G28310.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 7
--------------gttagtcatctggtcatt-taccggttattaagtatgtttgtcgagtatgtttttatcgaaattctctactggttttggcagGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT
                |  |  | | |||||| |  | | |  | | |   ||||  |  ||| || | |       | | | |   |    | |||||||| || || || ||  ||||||||||| ||||| ||||||||||||||||||| || |||||||| || ||||| |||||||||||||||||||| 
gtctgctactttgctctgatgctattgtcattctctcaggtgctcaat---tttgaaggatatcttctaaagatttatttatgcacatacatgtagGTGGTATGCCAAAAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATCTGGGATGAGGACCTTGGGGTGGAGCATTTCAATGCGGAG

upper sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g73970.1 (Oryza sativa), 3'ss of exon 7
gttagtcatctggtcatttaccggttattaagtatgtttg---tcgagtatgtttttatcgaaattctctactggttttggcagGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT
  ||  | |||| || |||        |||    ||| |    | ||   || || ||  || | | | |  |     | | |||||||| || || || || || || |||||| | ||| || ||||||||||||||||||| ||||| || ||||||||||| |||||||| || || || 
-gtacac-tctgctcctttgatatcctttataattgtctaaattggaaggtgattctaaagatactgttttgtttaaattgtagGTGGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTACATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAG

upper sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g19510.2 (Oryza sativa), 3'ss of exon 7
-------------------gttagtcatctggt-catttaccgg-ttattaagtatgtttgtcgagtatgtttttat-cgaaattctctactggttttggc--agGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT
                    ||| | || || |   | | | |  |   |  | || ||||  | | | || || || |   ||   ||  | |||||  |  |||||||| || ||| ||||||||||||||||||||||  |    ||||| |||||||| || |||||||| || || || || |||||||||||||| || 
gtaggtaaaggttattgttattattaatatgttatctgtgctgaatccatttgaatttttgctgtgaa-gtcttaatactgtatgtacttgttgttttacctaagGTGGTATGCAAAGCGGTTTTTGCATCCTGATGTTGTTGCCCGATATGACTACATATTCATCTGGGATGAGGACCTAGGTGTTGAGCATTTCAATGCAGAG

upper sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g68260.1 (Oryza sativa), 3'ss of exon 6
----------------------gttagtcatctggtcatttaccggttattaagtatgt--ttgtcgagtatgtttttatcgaaattctctactggttttggca-gGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT
                      |||     | |  |||| | |  |||    | |||||  ||| | |  |     | |  |   | ||||  |  |||   || ||||||| || ||||| ||||| ||||||||| ||||  |  | ||||| ||||||||||| |||||||| |||||  | ||  | ||||||||||| || 
gtaaattattgtaacagatcctgttg--tgttttttcatcttctagtttagcactatgtatttgacaaccaaaggctaagtgttttactctttttttttatacaagGTGGTATGCCAAGAGATTTTTACATCCTGATATTGTTGCCCCGTATGACTACATATTTATCTGGGATGAGGATCTAAGTGTACAACATTTCAATGCAGAG

upper sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 7
---------gttagtcatctggtcatttaccggttattaagtatgtttgtcgagtatgtttttat-cgaaattctctactggttttggca------gGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT
          || ||  ||| ||    |    |   || | |   ||  |     ||| | |  | | || || | |  | ||     ||      ||||||| || ||||| ||  ||||||||||| ||||| ||||||||||||||||||| || |||||||| || ||||| || || ||||| ||||| || 
gtgagtttcatttgtgctctagtgtactgttcgcagttcaattgcttaatttgaaatgatctagtgctaatttttttgtttgtgcacacaactctagGTGGTATGCCAAGAGATTCCTGCATCCTGATATTGTGGCAGCTTATGAGTACATATTCATTTGGGATGAGGACCTTGGGGTTGAACATTTTAATGCAGAG

upper sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM5G801369_T02 (Zea mays), 3'ss of exon 7
--------------gttagtcatctg-gtcatttaccggttattaagtat------gtttgtcgagtatgtttttatcgaaattctctactggttttggcagGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT
               | | |  |||| ||     |  ||    | ||| |       |||||| |  |    ||   | || || | |   | ||     |||||||| || ||  | ||| | ||||||||  ||||  |    || || ||||||||||| ||||||||||||||||| || || ||||| ||||| || 
cctaaacaattcctatgaattttctgcgttccaaaggggcccctcagtctctatgcatttgtccatcaaaggttg--caaacttatttctcgtttacccaagGTGGTATGCCAAACGATTTCTACATCCTGACATTGTTGCCCGCTACGACTACATATTTATCTGGGATGAAGATCTTGGTGTCGAACATTTTAATGCAGAG

upper sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 7
-------------------------------------------------------------------------------------------------------gttagtcatctggtcat--ttaccggttattaagta--tgtttgtcgagtatgtttttat-cgaaattctc-tact-ggttttg-gcagGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT
                                                                                                        | |   | ||  ||||  |||   || || |  |   || |   |   | || |||||| | |  ||||| ||||   | ||| |||||||||| || || || |||||||| |||||| | || ||||||||||| || || ||||| |||||||||||||||||||| || || |||||||| || 
gtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctatttttttgtgatcacatttaactttggaattcttaaaagaccttatcattcttaggagtgatgaccttattgctatactcctttgcttttatacaattttctcgtactcaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC

upper sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------------------------------------------gttagtcatctggtcatttaccggttattaagtatgtttgtcgagtatgtttttatcgaaattctcta---ctggttttg-gcagGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT
                                                                                                |  | || |        ||| |  || ||| |  || |   |   | || ||||||  || |||        |  | ||| |||||||||| || || || |||||||| |||||| | || ||||||||||| || || ||||| |||||||||||||||||||| || || |||||||| || 
gtatagttttctccaatcatttttttgcatttaacttatgaaagtcataggtattggacatgggaagcctattttttggtgatcacatttaactttggaattcttaaaagaccttatca-ttcttaggagtgatgaccttat-tgcttttatgcaatttcctcgtacttaatgttgtgcagGTGGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGAC

upper sequence: AT2G28310.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 7
----------------gttagtcat-ctggtcatttaccggttattaa--gt--atgtttgtcgagtatgtttttatcgaaattctctactggttttggcagGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT
                 || |  |  |||    |||  | | |    |  ||  ||  || | |     |||| |||  | |   ||   ||  ||  |||||||||| || || ||||| |||||||||||||||||  | |||||||| || || ||||||||||||||||| || |  ||  |||| |||||||  || 
ggagagacacggcattattggctaagctgaaactttttctgctgcagatagttaatactttttgtcctagtttatattcatagattcccatgtatt--gcagGTGGTATGCAAAAAGGTTCTTGCATCCTGATGTTGTTGCTGCTTATGAATATATTTTTATATGGGATGAAGACCTAGATGTAAAGCACTTCAATGGAGAG

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|124931092|gb|EL008484.1|EL008484
EST:     GAGTGGTCGAAGAGCGCGATTCATATTAGTACAAGAAAGCAAACAAAATG                         GTGGTACGCGAAG
genomic: GAGTGGTCGAAGAGCGCGATTCATATTAGTACAAGAAAGCAAACAAAATGgttagtcatc ... gttttggcagGTGGTACGCGAAG
EST: gi|164140949|gb|ES035071.1|ES035071
EST:     GAGTGGTCGAAGAGCGCGATTCATATTAGTACAAGAAAGCAAACAAAATG                         GTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTAT
genomic: GAGTGGTCGAAGAGCGCGATTCATATTAGTACAAGAAAGCAAACAAAATGgttagtcatc ... gttttggcagGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaagtatgtttgtcgagtatgtttttatcgaaattctctactggttttggcagGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT
                       tttttatcgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtcatctggtcatttaccggttattaagtatgtttgtcgagtatgtttttatcgaaattctctactggttttggcagGTGGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA