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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattacttattctctgtgtttgtttcaccttggagatgatattgttggtttaagtctttgttattgtatttggcagATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACCAGATTGTGAACAAGGATGGTAAGCCATACATTCAAGTCAAGATCAAGGATGGT

Basic information

species Arabidopsis thaliana
transcript AT5G28540.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 2
------gtaatt-acttattctctgtgtttgtttcaccttggagatga-tattgttggtttaagtctttgttattgtatttggcagATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACCAGATTGTGAACAAGGATGGTAAGCCATACATTCAAGTCAAGATCAAGGATGGT
      | | || ||    |    |   || ||||   |||  ||| | |  ||   | |     || | | ||| |  ||| ||| ||||| || ||||| ||||| | ||| | ||||||||| || ||| |||||||||||||||| |||||||| |||||||| ||||||||||||||||| 
gtaatggcactttaccctatgctcgctcttatttcctgttgttgatcactgctgcctgatctgacctgtataattattcttg-cagGTTTGAAGACAAGGAAGTTCAGAGGGACATGAAACTTGTCCCCTACAAGATTGTGAACAAGGACGGTAAGCCCTACATTCAGGTCAAGATCAAGGATGGA

upper sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 2
gtaattacttattctc-----tgtgt---ttgtttcaccttggagatgatattgttggtttaagtctttgttat-tgtatttggcagATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACCAGATTGTGAACAAGGATGGTAAGCCATACATTCAAGTCAAGATCAAGGATGGT
||| |  ||   || |     ||  |   || ||||  || |  |  | |  |||  |      |   ||| ||    |||    || ||| |||||||||| || || | ||| | ||||||||| || ||| ||||| | ||||||||||| |||||||||||||| ||||||||||||||||| 
gtagtgcctctctcccacaattgcttctattatttcgtctcgctgtgggttatgtctggcgtcttacctgtaatgcccattgcttagGTTTCAGGATAAGGAAGTCCAGAGGGACATGAAACTTGTCCCCTACAAGATTATTAACAAGGATGGCAAGCCATACATTCAGGTCAAGATCAAGGATGGG

upper sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 2
----------------gtaattacttattctctgtgtttgtttcaccttggagatgatattgttggtttaagtctt-tgttattgtatttggc-agATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACCAGATTGTGAACAAGGATGGTAAGCCATACATTCAAGTCAAGATCAAGGATGGT
                  | |||||| |  |   | || || ||    ||| | |  |  ||  |  |||| | |  |  |     ||||    || || | ||| ||||| || || | ||| | ||||||||| || ||| ||||| | ||||||||||| ||||| |||||||| ||||||||||||||||| 
gtaacacctctctcctacagttacttctgttgaat-ttcgtctcgttgtgg-gttatttctggcgtcttaactttagtaatgccccatttatttagGTTCGCGGACAAGGAAGTCCAGAGGGACATGAAACTTGTTCCCTACAAGATTATTAACAAGGATGGCAAGCCCTACATTCAGGTCAAGATCAAGGATGGG

upper sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 2
gtaattacttattctctgtgtttgtttcaccttggagatgatattgttggtttaagtctttgtta-ttgta---tttggcagATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACCAGATTGTGAACAAGGATGGTAAGCCATACATTCAAGTCAAGATCAAGGATGGT
||||  ||||  ||    ||||  |||        |  |||| | || || | || | ||  | | ||| |   ||| |||| || || |||||||| |||||||| || | ||| ||||| |||||  ||||||| ||||||||||| || || |||||||| || || || |||||||||
gtaag-acttgctcaagttgttgatttttgac--aatttgatttggtgggatcaattgttactgacttgcatctttttgcagGTTCGAAGATAAGGAAGTTCAAAAAGACATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATTCAGGTGAAAATTAAGGATGGT

upper sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 2
gtaattacttattctctgtgtttgtttcaccttggagatgatattgttggtttaagtctttgttattgtatttggcagATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACCAGATTGTGAACAAGGATGGTAAGCCATACATTCAAGTCAAGATCAAGGATGGT
||||  ||||| ||    || || ||     || ||  ||||    |   |           ||  | | |||| ||| || || |||||||| |||||||  |||| ||| ||||| |||||  ||||||| ||||||||||| || || ||||| ||||| || || |||||||||
gtaag-acttactcaagttgatttttgacaatttgatttgatgggatcaatggtgactgacatttatctttttg-cagGTTCGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTCAACAAGGATGGAAAACCTTACATACAAGTGAAAATTAAGGATGGT

upper sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 2
---gtaattacttattctctgtgtttgtttcaccttgga--gatgatattgttggtttaagtctttgttattgtatttggcagATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACCAGATTGTGAACAAGGATGGTAAGCCATACATTCAAGTCAAGATCAAGGATGGT
     | ||||| |   | |   ||| |  ||  |||    ||||  ||   ||||    | ||    | |    ||| |||| ||||| |||||||| |||||||  |||| ||| ||||| |||||  ||||||| ||||||||||| || || ||||| || || || || |||||||||
gtaagacttactcaagttgttgatttttgacaatttgatttgatgggatcaatggt----gactgacatgtatccttttgcagGTTTGAAGATAAGGAAGTTCAAAGAGATATGAAGCTTGTTCCTTATAAGATTGTTAACAAGGATGGAAAACCTTACATACAGGTGAAAATTAAGGATGGT

upper sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 3'ss of exon 2
---------gtaattactta---ttctctgtgtttgtttcaccttgg---agatgatattgttggtttaagtctttgttattgtatttggcagATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACCAGATTGTGAACAAGGATGGTAAGCCATACATTCAAGTCAAGATCAAGGATGGT
          ||  ||  ||    | |  || | ||  |    || |     | |  | | || | | | |  |||   ||    |||| ||| ||||| |||||||||||||| ||||| | ||| ||||| || ||| | ||||| ||||||||||| ||||| |||||||||||||||||||||||||||
gtaatacgtctatctatctaaagcttttggtctatgcattgtattagttggcaaggaactttttgctgaggctttta--atcacttttgacagGTTTGAAGATAAGGAGGTTCAGAAGGACATGAAGCTTGTTCCGTACAACATTGTTAACAAGGATGGGAAGCCTTACATTCAAGTCAAGATCAAGGATGGT

upper sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 2
----------------gtaat-tacttattctctgtgtttgtttcaccttggag--------atgatattgttggtttaagtctttgt-tattgtatttg--gcagATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACCAGATTGTGAACAAGGATGGTAAGCCATACATTCAAGTCAAGATCAAGGATGGT
                 |||| | |||  | |   | || |||   | || ||         || |      |    |   | ||||  | |||| |||   | |||||||| ||||| |||||||||||||| | ||| ||| | || | | |||| |||||||||||||| |||||||| || ||||||||||| |||||||| 
gtatgtgataaatcctttaatctcctttctgttcatattcgttgatcttttgaatgaagcccatcaaggctctaacctggttttttgccttttgttttttctgtagATTTGATGATAAAGAGGTTCAAAAGGACATGAAGCTTTTCCCATTCAAGATCGTGAACAAGGATGGAAAGCCATATATACAAGTCAAGATTAAGGATGGG

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|164027679|gb|ES160255.1|ES160255
EST:     GTTAATCCAGAGAGGACTGTCTTCGACGTTAAGAGATTGATCGGGCGAAA                         ATTTGAGGACAAGGAGGTTCAAAAGGACAGGAAACTTGTACCTTACC
genomic: GTTAATCCAGAGAGGACTGTCTTCGACGTTAAGAGATTGATCGGGCGAAAgtaattactt ... tatttggcagATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACC
EST: gi|124860151|gb|EH944588.1|EH944588
EST:     TTAAGAGATTGATCGGGCGAAA                         ATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACCAGAT
genomic: TTAAGAGATTGATCGGGCGAAAgtaattactt ... tatttggcagATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACCAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcaccttggagatgatattgttggtttaagtctttgttattgtatttggcagATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACCAGATTGTGAACAAGGATGGTAAGCCATACATTCAAGTCAAGATCAAGGATGGT
                                   tttgttattgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattacttattctctgtgtttgtttcaccttggagatgatattgttggtttaagtctttgttattgtatttggcagATTTGAGGATAAGGAGGTTCAAAAGGATAGGAAACTTGTACCTTACCAGATTGTGAACAAGGATGGTAAGCCATACATTCAAGTCAAGATCAAGGATGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG