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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactccagttttttctcttctgttatactatattcagttcaatcatcatgcctaggatcaatcaatcaataaatcctaattaagccaaacaacatatatatgatatgatatgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGGAAGATCATACTGCTCCGATACTTCAACCCTGTTGGAGCTCACCCAAGCG

Basic information

species Oryza sativa
transcript LOC_Os05g51670.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51670.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G038598_T02 (Zea mays), 3'ss of exon 4
gtactccagttttttctcttctgttatactatattcagttcaatc-atcatgcctaggatcaatcaatcaataaatc-ctaattaagccaaacaacatat---atatgat-atgatatgat----tgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGGAAGATCATACTGCTCCGATACTTCAACCCTGTTGGAGCTCACCCAAGCG
    |||  | || | |||||    || |||    |||  |||||   | |      | ||||   ||||  | |    || |||    ||| || | |    ||||||| ||||     |    ||||||| || || |||||||| ||||| ||  | ||   ||| |||||  |||||||||||||||||||| | ||||||||||| ||||| ||||| |||||||
--gttcc--tcttctgtcttcaaagattcta-gcacagaccaatccggccttttgttgttcaaatgatcatgacacaattagttacataaaaaaataaaagtaatatgatgatgacgccgtgctctgcagCTTGTGATTGAAGACATCTGCCGCGACGTCCACCGCTCCGACCCCGACTGGAAGATCATACTGCTCAGGTACTTCAACCCCGTTGGCGCTCATCCAAGCG
















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|218494764|gb|FG965511.1|FG965511
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|218481702|gb|FG969560.1|FG969560
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|33681007|gb|CF309246.1|CF309246
EST:     GCACTGAAGAATCCCCACCTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|38480755|gb|CF964844.1|CF964844
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAGCAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGANCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|58588964|gb|CF987272.1|CF987272
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACGGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|58690277|gb|CK078964.1|CK078964
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|33798368|gb|CF325041.1|CF325041
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTC
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTC
EST: gi|218494080|gb|FG967420.1|FG967420
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|29621545|gb|CB626556.1|CB626556
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|33693008|gb|CF321247.1|CF321247
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCC
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCC
EST: gi|218497254|gb|FG946482.1|FG946482
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|33682645|gb|CF310884.1|CF310884
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|33680697|gb|CF308936.1|CF308936
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCCGGGATCTGCATGCCTC
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCC-GGGATCTGCATGCCTC
EST: gi|33692560|gb|CF320799.1|CF320799
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTC
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTC
EST: gi|29684846|gb|CB681121.1|CB681121
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|33679540|gb|CF307779.1|CF307779
EST:     GCACTGGAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTC
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTC
EST: gi|33661837|gb|CF292804.1|CF292804
EST:     ACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: ACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|33686980|gb|CF315219.1|CF315219
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|218488558|gb|FG963890.1|FG963890
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|33681223|gb|CF309462.1|CF309462
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTC
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTC
EST: gi|218482145|gb|FG968615.1|FG968615
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|33685111|gb|CF313350.1|CF313350
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|218505351|gb|FG968507.1|FG968507
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|33688841|gb|CF317080.1|CF317080
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGA
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGA
EST: gi|29662182|gb|CB658457.1|CB658457
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|33686993|gb|CF315232.1|CF315232
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGA
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGA
EST: gi|33684323|gb|CF312562.1|CF312562
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACCATGTGCCGGGATCTGCATGCCTC
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGAC-ATGTGCCGGGATCTGCATGCCTC
EST: gi|218501599|gb|FG966518.1|FG966518
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
EST: gi|58689696|gb|CK078383.1|CK078383
EST:     GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAG                         CTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG
genomic: GCACTGAAGAATCCCCACTTTGTGCAATGAACCCCTACGGCAGAACAAAGgtactccagt ... atgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaataaatcctaattaagccaaacaacatatatatgatatgatatgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGGAAGATCATACTGCTCCGATACTTCAACCCTGTTGGAGCTCACCCAAGCG
         tcctaat  putative branch site (score: 2)
                             atatatatgatatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactccagttttttctcttctgttatactatattcagttcaatcatcatgcctaggatcaatcaatcaataaatcctaattaagccaaacaacatatatatgatatgatatgattgcagCTGGTAATCGAAGACATGTGCCGGGATCTGCATGCCTCAGACCCAAACTGGAAGATCATACTGCTCCGATACTTCAACCCTGTTGGAGCTCACCCAAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA