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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctcagtaagataatattaatttcatcatacatctatgtaggtttgtagaaaatgataaaagcagcaagcatatattgttagggagtaacatac...

Basic information

species Oryza sativa
transcript LOC_Os06g09330.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g09330.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G116919_T02 (Zea mays), 5'ss of exon 7
ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgta-----attgctcagtaagataatattaatttcatcataca-tctatgtaggtttgtagaaaatgataaaagcagcaagcatatattgttagggagtaacatac
||||| ||||| ||||||||||||||||||| ||   |||| |  |||||||| ||||||||||| |||||||||| |||||| |||||||||||     ||| ||| | | | || | | | | | | |||    | | |||||   |||   |||  |      |  || | | ||| || |    ||   |  | 
ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAGAGGCGTTTAGCAAAAGCTTCCCTTGTCTACAATTGTGAGAGgtagatgcatttctctgcaggcta-tttcattctgaccattttctttttgtagaactgttagaaactac-----ccacaggaacataatggtcattagcttctgaa

upper sequence: LOC_Os06g09330.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G177276_T01 (Zea mays), 5'ss of exon 8
ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgta-----attgctcagtaagataatattaatttcatcataca-tctatgtaggtttgtagaaaatgat----aaaagcagcaagcatatattgttagggagtaacatac
||||| ||||| ||||||||||||||||||| ||   |||| |  |||||||||||||||||||| ||||||||||| ||||| |||||||||||     ||| ||| | | | || | | | | | | |||    | | |||||    ||   |||        |  ||||| | ||  ||    ||  | |         
ATGGACGATGCACTGACAACTGGAAGCATCAAGACGTCAGATGCAGAAAAGAGACGTTTAGCAAAAGCTTCCCTTGCTTACAATTGTGAGAGgtagatacatttctctgcaggcta-tttcattctgaccattttctttctgtagaaccgttacaaacccccttcaggagcagaatgcccattagcttctgaa---------

upper sequence: LOC_Os06g09330.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G453855_T03 (Zea mays), 5'ss of exon 5
ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgta-----attgctcagtaagataatattaatttcatcataca-tctatgtaggtttgtagaaaatgataaaagcagcaagcatatattgttagggagtaacatac
||||| ||||| ||||||||||||||||||| ||   |||| |  |||||||| ||||||||||| ||||||||||||||||| |||||||||||     ||| ||| | | | || | | | | | | |||    | | |||||   |||   |||  |      |||  | |||| || || |     |       
ATGGACGATGCACTGACAACTGGAAGCATCAAGACATCAGATGCAGAAAAGAGGCGTTTAGCAAAAGCTTCCCTTGCCTACAATTGTGAGAGgtagatgcatttctctgcaggcta-tttcattctgaccattttctttttgtagaactgttagaaactacccccacag-gaacata-atggtcattagcttctg---

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|66913939|gb|CX100787.1|CX100787
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCGTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|87015788|gb|CI279540.1|CI279540
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|87010686|gb|CI312378.1|CI312378
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|86602343|gb|CI262812.1|CI262812
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|86495662|gb|CI138295.1|CI138295
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|86599367|gb|CI251325.1|CI251325
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|86514651|gb|CI157284.1|CI157284
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CCATAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACTTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|86855623|gb|CI268950.1|CI268950
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACCTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|88832979|gb|CI369869.1|CI369869
EST:     GGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|88995570|gb|CI022893.1|CI022893
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|88206366|gb|CI206215.1|CI206215
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|86543106|gb|CI183312.1|CI183312
EST:     TAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: TAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|88201919|gb|CI202274.1|CI202274
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|86863829|gb|CI332842.1|CI332842
EST:     CAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: CAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|88281529|gb|CI402925.1|CI402925
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCAGTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|87035120|gb|CI189743.1|CI189743
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|88836287|gb|CI371392.1|CI371392
EST:     CTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: CTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|86543752|gb|CI183958.1|CI183958
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|88506399|gb|CI433905.1|CI433905
EST:     CTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: CTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|86876250|gb|CI318325.1|CI318325
EST:     GGGGAAAAGAGACGTTTACCAAAGGCTTCCC-TGCCTACAACTGTGAGAG                         CAAAAA-TGCCCTCACTTCA-GAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|88201904|gb|CI202259.1|CI202259
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|89186387|gb|CI262219.1|CI262219
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|88837493|gb|CI078853.1|CI078853
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTNGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|86543032|gb|CI183238.1|CI183238
EST:     AGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: AGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|88486749|gb|CI424020.1|CI424020
EST:     AGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: AGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|87035496|gb|CI190118.1|CI190118
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|88223516|gb|CI223365.1|CI223365
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|218478139|gb|FG953402.1|FG953402
EST:     CCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: CCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|88511500|gb|CI439006.1|CI439006
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|88201307|gb|CI201662.1|CI201662
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|88968003|gb|CI098245.1|CI098245
EST:     GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTNGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|86543063|gb|CI183269.1|CI183269
EST:     GGGGTAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: GGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA
EST: gi|88837828|gb|CI371406.1|CI371406
EST:     CTTCCCTTGCCTACAACTGTGAGAG                         CAAAAATTGCCCTCACTTCAGGGAAATGTTTCCAGAGTACGTCGAGAAATA
genomic: CTTCCCTTGCCTACAACTGTGAGAGgtaattgctc ... gtttccacagCAAAAATTGCCCTCACTTCAGGAAAATGTTTCCAGAGTACGTCGAGAAATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGATGATGCTCTGACAACTGGAAGCATCAGGAGTACAGAGGGGGAAAAGAGACGTTTAGCAAAGGCTTCCCTTGCCTACAACTGTGAGAGgtaattgctcagtaagataatattaatttcatcatacatctatgtaggtttgtagaaaatgataaaagcagcaagcatatattgttagggagtaacatac

- - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG