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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttccatctccatggatctatctggataattgaaatagaaatagaattctgtgaagctgttaatgacatatgtttgttttttcagGGGCAAGATGTTGCTTTTGAACCAGCAAAGCTTCTTTGGCTTATCCAGAGGGATTTCCTGC

Basic information

species Oryza sativa
transcript LOC_Os03g58240.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G019361_T02 (Zea mays), 3'ss of exon 7
--------------------------------------------------------------------------------------------gtaatgttccatctcca-tggatctatctggataattgaaatagaaatagaattctgtgaagctgttaatgacatatgtttgttttttcagGGGCAAGATGTTGCTTTTGAACCAGCAAAGCTTCTTTGGCTTATCCAGAGGGATTTCCTGC
                                                                                            | |  ||        || || || |   ||  | ||  |    | ||||| |   ||   || | || |    | ||| |||||| ||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||| |
ttcatttttcgtgcctttctgtttggttataatcattttgatctggaaaactaacatttattctttttttgttatatgctgcatgtttgtgagcagagtgaaggtaacactgcatttgcgtgacttat-aagcctgcaataggaacatggatagttttttaatggaaatgcttgtttcttcAGGGGCAAGATGTTGCTTTTGAGCCAGCAAAGCTTCTCTGGCTTATCCAGAGGGATTTCCTCC

upper sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G019361_T01 (Zea mays), 3'ss of exon 7
---------------------------------------------------------------------------------------gtaatgttccatctcca-tggatctatctggataattgaaatagaaatagaattctgtgaagctgttaatgacatatgtttgttttttcagGGGCAAGATGTTGCTTTTGAACCAGCAAAGCTTCTTTGGCTTATCCAGAGGGATTTCCTGC
                                                                                       | |  ||        || || || |   ||  | ||  |    | ||||| |   ||   || | || |    | ||| |||||| ||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||| |
ttttcgtgcctttctgtttggttataatcattttgatctggaaaactaacatttattctttttttgttatatgctgcatgtttgtgagcagagtgaaggtaacactgcatttgcgtgacttat-aagcctgcaataggaacatggatagttttttaatggaaatgcttgtttcttcagGGGCAAGATGTTGCTTTTGAGCCAGCAAAGCTTCTCTGGCTTATCCAGAGGGATTTCCTCC

upper sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G305254_T07 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------------------------------------------------------gtaatgttccatctccatggatctatctggataattgaaatagaaatagaattctgtgaagctgttaatgacatatgtttgttttttcagGGGCAAGATGTTGCTTTTGAACCAGCAAAGCTTCTTTGGCTTATCCAGAGGGATTTCCTGC
                                                                                                              |||||  ||||  | |||| || |||  || |   | |||||| || |    | | |     | || |||  | ||| || | |  |||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||| |
gtttgctcatttcttttgtgcctttctgtttccatataatcattttgatctggaacactaacatttatcctttttttgttatatgctgcacttttgtgagcagagtgaaggtaatactccagtttcatgaat-tataaggctg--taaaataggaacatggatattt-----ttttgatgg-aaatgcttaTCT--TCAGGGGCAAGATGTTGCTTTTGAGCCAGCAAAGCTTCTCTGGCTTATCCAGAGGGATTTCCTCC

upper sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G321413_T01 (Zea mays), 3'ss of exon 1
----------gtaatgttccatctcca-tggatctatctggataattgaaatagaaatagaattctgtgaagctgttaatgacatatgtttgttttttcagGGGCAAGATGTTGCTTTTGAACCAGCAAAGCTTCTTTGGCTTATCCAGAGGGATTTCCTGC
          | |  ||        || || || |   ||  | ||  |    | ||||| |   ||   || | || |    | ||| |||||| ||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||| |
atgtttgtgagcagagtgaaggtaacactgcatttgcgtgacttat-aagcctgcaataggaacatggatagttttttaatggaaatgcttgtttcttcagGGGCAAGATGTTGCTTTTGAGCCAGCAAAGCTTCTCTGGCTTATCCAGAGGGATTTCCTCC

upper sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G305254_T04 (Zea mays), 3'ss of exon 7
-------------------------------------------------------------------------------------------------------------gtaatgttccatctccatggatctatctggataattgaaatagaaatagaattctgtgaagctgttaatgacatatgtttgttttttcagGGGCAAGATGTTGCTTTTGAACCAGCAAAGCTTCTTTGGCTTATCCAGAGGGATTTCCTGC
                                                                                                             |||||  ||||  | |||| || |||  || |   | |||||| || |    | | |     | || |||  | ||| || | |  |||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||| |
tttgctcatttcttttgtgcctttctgtttccatataatcattttgatctggaacactaacatttatcctttttttgttatatgctgcacttttgtgagcagagtgaaggtaatactccagtttcatgaat-tataaggctg--taaaataggaacatggatattt-----ttttgatgg-aaatgcttatCT--TCAGGGGCAAGATGTTGCTTTTGAGCCAGCAAAGCTTCTCTGGCTTATCCAGAGGGATTTCCTCC

upper sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G427677_T01 (Zea mays), 3'ss of exon 6
gtaatgttccatctccatggatctatctggataattgaaatagaaatagaattctgtgaagctgttaatgacatatgtttgttttttcagGGGCAAGATGTTGCTTTTGAACCAGCAAAGCTTCTTTGGCTTATCCAGAGGGATTTCCTGC
||||   | ||    | |   |||     |||   |||||||    ||||| | | | ||      ||| |  | |||  |  | | ||||||||||||||||||||||| ||||| || ||||| ||| | |||||||||||||| || |
gtaaaacttcactaacctacgtct---cagatttatgaaata----tagaagtatatcaa------aatcatgt-tgtggggctctgcagGGGCAAGATGTTGCTTTTGAGCCAGCCAAACTTCTGTGGTTGATCCAGAGGGATTTTCTCC

upper sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaatgttccatctccatggatctatctggataattgaaatagaaatagaattctgtgaagct--gttaatgacatatgtttgttttttcagGGGCAAGATGTTGCTTTTGAACCAGCAAAGCTTCTTTGGCTTATCCAGAGGGATTTCCTGC
       |  | |   | |||         ||  ||||   |    | | || ||   || ||  |||  |||  | | | | |  | | ||||  |||||||||||||||||||  |||||||||| |||||||||||| | ||||| ||||
------gtataccctaacggaatggctgttattcttgatcca----tggcatccttcaaaacttcgtttctgatttttatatatcctgt-agGGTGAAGATGTTGCTTTTGAACCGTCAAAGCTTCTGTGGCTTATCCAGCGTGATTTTCTGC

upper sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv07s0141g00110.t01 (Vitis vinifera), 3'ss of exon 8
-------------------------------gtaatgttccatctccatggatctatctggataattgaaatagaaatagaattct----gtgaagctg-ttaatgacatatgtttgttt-----tttcagGGGCAAGATGTTGCTTTTGAACCAGCAAAGCTTCTTTGGCTTATCCAGAGGGATTTCCTGC
                                |  |  |  || | |   | | | |    |||| |       |||  |||| ||     | |||||| |   |  | | | ||||  |     || ||||| ||||||||||| |||||||| || |||||||| |||||||||||  | ||||| || |
gtaatcttcaagccagttttattttctttttttgcttatgtatattctctggtttgttgtaataaatctttctaaaagtgaatgcttttaataaagctgatctttttcttgtttttgaatggatattgcagGGACAAGATGTTGCCTTTGAACCTGCTAAGCTTCTGTGGCTTATCCAACGTGATTTTCTAC

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|29636549|gb|CB641558.1|CB641558
EST:     AGAATTCTATGGAAGAGTGAAG
genomic: AGAATTCTATGGAAGAGTGAAG
EST: gi|29629845|gb|CB634854.1|CB634854
EST:     AGAATTCTATGGAAGAGTGAAG
genomic: AGAATTCTATGGAAGAGTGAAG
EST: gi|29666666|gb|CB662941.1|CB662941
EST:     AGAATTCTATGGAAGAGTGAAG
genomic: AGAATTCTATGGAAGAGTGAAG
EST: gi|29629844|gb|CB634853.1|CB634853
EST:     AGAATTCTATGGAAGAGTGAAG
genomic: AGAATTCTATGGAAGAGTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatagaaatagaattctgtgaagctgttaatgacatatgtttgttttttcagGGGCAAGATGTTGCTTTTGAACCAGCAAAGCTTCTTTGGCTTATCCAGAGGGATTTCCTGC
                           tgttaat  putative branch site (score: 3)
                                          tttgttttttc  putative PPT
                                     atatgtttgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgttccatctccatggatctatctggataattgaaatagaaatagaattctgtgaagctgttaatgacatatgtttgttttttcagGGGCAAGATGTTGCTTTTGAACCAGCAAAGCTTCTTTGGCTTATCCAGAGGGATTTCCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG