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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgaatcactcttttttatattgcctatgattcagcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA

Basic information

species Oryza sativa
transcript LOC_Os07g47530.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G157621_T02 (Zea mays), 3'ss of exon 22
tgtgaatcactcttttttatattgcctatgattcagcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
 || | | | | | ||     |  |  |||||    |    |  ||| ||   | | || | |  | | |   ||   | || |  |||         ||||||||||||||||||||||| | ||||| |||||||||||||| || ||||||||||||||||||||||||||||| || ||||||||||| || ||||
-gttagtgattttcttaacggtcactgatgatatgccta--tgacataataa-gttgtagcttactcattgatttgtgtcctgtatatt---------agGTTGATGGCATGCTGGGTAGACGTGAGAATCCAGGGGAACATGAGGCCATGCGCAAGATGAAAAATGAGTTTATGGTGAACTGGGATGGTCTTAGGACAA

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 18
tgtgaatcactcttt-tttatattgcctatgattca-gcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
  ||||  |||     |||| ||  | |||  || | |   ||||  |||  |||  ||  |     | |  |   |   ||   |       || | | |||||||| | ||||| || ||| | || |||||  | || ||||| |||||||| || |||||||||||||||||||||||||||||||||||| | ||||
--tgaagaactaaacatttaaatctcatattttttatggtagctactatggattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTTGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 19
-tgtgaatcactcttttttatattgcctatgatt--cagcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
   | || ||   |    | || ||  | |  ||   |||      | ||  | || ||||    | |   || | | | || || |   ||  |  | | |||||||| | ||| | || ||| | || || || || || ||||| |||||||| || ||||| ||||| || ||||| |||||||||||| || ||||||
ggcttaaacatattcaaatctagtgtttttctttggtagcttctacggatattcttagtttcaattatct-gtgtttgatttgctgt--gttactgatggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAGCATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGCGAACAA

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 23
tgtgaatcactcttttttatattgcctatgattcagcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
 || |  |  |  | |  || || | ||   |  | ||    | || | |      | |  | ||  |   |  ||     |          || | ||||||||| ||||| |||| || ||||| || || ||||| ||||| || ||||| |||||||||||||| || ||||| |||||||||||  |  | ||||
-gtaagccttttgtataaatgtt-cttagtttgtatcaattcaaca-gctgaaaaataaatcagtgaaaactagtatggctt---------cttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACAA

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 6
tgtgaatcactcttttttatat-tgcctatgattca-gcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
      | |  |||||  | |  ||  | | |||         |    || |      | |  | ||| |       |  || |||   |||  || | ||||||||| ||||| |||| || ||||| || || ||||| ||||| || ||||| |||||||||||||| || ||||| || ||||||||  |  | ||||
-----gtaagccttttgcacaaatgtttttaatttgtatcaattcatctgctgcaaaataaatcagttaa-------aacttgtatggcttc--ttgtatagGTTGATAGCATGTTGGGCAGGAGGGAAAATCCTGGGGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAACTGGGATGGCTTACGCACAA

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 19
tgtgaatcactcttttttatattgcctatgattcagcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
                   ||   | | | | | |  |||   | ||  |||||  ||      |||  | |     || ||| |  || ||||    |||||||  ||||| ||||| | ||||| |||||||| || ||||| || ||||| |||||||||||||| || ||||| |||||||||||  |  | || |
------------------gtaagccttttaactta--agg---gtattgttttgtattgattcattggatgtaac-tttactagc--tttgtttc---agGTTGACAGCATGTTGGGTCGTAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGCTTACGCACGA

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 22
tgtgaatcactcttt-tttatattgcctatgattcagca-ggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
  ||||   ||     |||| ||  || ||  || |  |  ||||  |||| |||  ||  |     | |  |   |   ||   |       || | | |||||||| | ||||| || ||| | || |||||  | || ||||| |||||||| || |||||||||||||||||||||||||||||||||||| | ||||
--tgaagacctaaacatttaaatctccaattttttatgatagctactatgaattttcttagtttcaattatctgtgttgatttgttgtggcaattgtggcagGTTGATAGTATGCTAGGGAGACGTGAAAACCCTAGTGAGCATGAGGCTATGCGAAAAATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGCGTACAA

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 21
tgtgaatcactcttttttatattgcctatgattcagcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
                   ||  |||| | |  ||   |  | |  |  | ||| || ||    |  |  |  |||||  ||         || ||  |||||||  ||||| ||||| | ||||| |||||||| || ||||| || ||||| |||||||||||||| || ||||| |||||||||||  |  | || |
------------------gtaa-gccttttaaccaagggtattgtgttgtattgattcattgaatataact--ttactagct---------ttgtttcagGTTGACAGCATGTTGGGTCGGAGGGAAAACCCAGGAGAGCATGAGGCCATGCGAAAGATGAAAAATGAATTCATGGTGAATTGGGATGGGTTACGCACGA

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 19
tgtgaatcactcttttttatattgcctatgattcagcaggctagcatg---attttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
    ||| |   ||    || | |  | |   |  |   |||   |     ||| | | ||    |  |  || | | | ||  | |       |  | | |||||||| | ||| | || ||| | || || || || |||||||| |||||||| || ||||| ||||| || ||||| |||||||||||| |||||||||
---aaatgagcattcagaatctagtgtttttctttggtagcttctacagatattcttgctttcaattatctgtgtttgatttgttttgtgacattggtggcagGTTGATAGTATGTTAGGAAGACGTGAAAATCCTGGTGAACATGAGGCTATGCGTAAAATGAAGAATGAATTCATGGTTAATTGGGATGGTTTGAGAACAA

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
lower sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 21
tgtgaatcactcttttttatattgcctatgattc----agcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgt--ttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
  |||   |   |  |  |  ||    |    ||    | | |  ||  |   ||    ||| || |  ||| | ||||   ||  |     ||    || ||||||||||| |||||||||| ||| | ||||| ||||| ||||||||||||||||| |||||||| || || || ||| |||| ||||| ||  |  | ||||
-atgaggtatgttgctagacgttaagaacagctctcatacctgtttattacagttcc--tttttctttctgaatatctt---ttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 22
tgtgaatcactcttttttat-attgcctatgattcagcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgt--ttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
 ||   |  ||     |||  |    || | || |  | |  ||  |   ||    ||| || |  ||| | ||||   ||  |     ||    || ||||||||||| |||||||||| ||| | ||||| ||||| ||||||||||||||||| |||||||| || || || ||| |||| ||||| ||  |  | ||||
-gtatgttgctagacgttaagaacagctctcatac--ctgtttattacagttcc--tttttctttctgaatatctt---ttgaacgggatcaaaattatgtagGTTGATAGCATGCTGGGAAGACGTGAGAATCCAGGAGAACATGAAGCTATGCGTAAGATGAAGAACGAATTCATGATAAACTGGGACGGCTTACGCACAA

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 22
-------------tgtgaatcactcttttttatattgcctatgattcagcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
             | | ||  |   || | |   ||  ||   |      | || ||  |   |||  | ||   | | ||  |  | |  || |    | || || ||  |||||||| ||||| |||||||| | || || ||||||||||||||||||||||| |||||||| || ||||| |||||||| ||||||||| | |||||||
gtatgtttgaagatattaaaaagcgttctctg--ttctctcccacctttgaagccagtct---ttttatgtactttctcgatctgatga--ttgtggaaaatcattatt-cagGTTGATAGCATGTTGGGTAGACGTGAAAATCCAGGGGAACATGAAGCTATGCGTAAGATGAAGAACGAGTTCATGGTAAACTGGGATGGTTTAAGAACAA

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 22
--------------------------------------------------------------------------------tgtgaatcactcttt--tttatattgcctatgattcagcaggctagcatgattttggtttatcctgttgagtttcttactttctatcca--ttcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
                                                                                ||    | ||| ||   |   | |        |||| |     |||  |  || |  ||| ||||||| |     ||| | |  |   |  ||  || ||  |||||||  ||||| | || ||| | || || ||||| ||||||||||||||| | || ||||| |||||||| ||||| || |||||||| ||  | ||||
gtaagttgaataaatctttaaattcatccacaacttttgctataatgttcctcactctttttatgggtccatggatttagtgacggtaactgttcaatccttttaattcgccattctgatctttagtttctttcttcttt-tcctgttaaaaaatttattgttaacttagatttattgtttcagGTTGACAGCATGTTAGGGAGACGTGAAAATCCAGGAGAACATGAAGCTATGAGGAAAATGAAGAATGAGTTCATGGTGAACTGGGATGGCCTACGTACAA

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 23
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 23
tgtgaatcactcttttttatattgcctatgattcagcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
                 |    | | ||| | ||     | |   ||  | || | ||   || |   | ||  ||  |||| |   || | | ||  |||||||| ||||||||||  | |||||||| |||||||||||||| || ||||| ||||||||||| || |||||||| || ||||||||  || | ||||
----------------gtgagcttcatataactctttttgtttatatattgtttgcttcctctct---gcttgctatattcttt--gtttggtctt--agGTTGATAGCATGCTGGGCCGGAGGGAGAATCCAGGGGAACATGAGGCCATGCGTAAGATGAAAAACGAATTTATGGTCAACTGGGATGGCTTGCGCACAA

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|29664460|gb|CB660735.1|CB660735
EST:     TGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG                         GTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATG
genomic: TGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAGgtcagtcaac ... gtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATG
EST: gi|58688870|gb|CK077557.1|CK077557
EST:     TGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG                         GTTGATGGCATGCTGGGTAGACGGGAGAACCCAGGGGAACATGAAGCTATG
genomic: TGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAGgtcagtcaac ... gtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATG
EST: gi|29669556|gb|CB665831.1|CB665831
EST:     TGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAG                         GTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATG
genomic: TGTTTTCACTTGCAAGCAAAATTGCTCCTAGTGTCATTTTTGTGGATGAGgtcagtcaac ... gtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA
                         ttcttac  putative branch site (score: 2)
                        tttcttactttctatc  CT-rich tract
                                              tttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgaatcactcttttttatattgcctatgattcagcaggctagcatgattttggtttatcctgttgagtttcttactttctatccattcgtttttgtagGTTGATGGCATGCTGGGTAGAAGGGAGAACCCAGGGGAACATGAAGCTATGCGCAAGATGAAAAATGAGTTTATGGTAAATTGGGATGGTCTGAGAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
-gtgaatc
- - - - - - - - - - - - - - tgattca
- - - - - - - - - - - - - - - - - -gcaggct
- - - - - - - - - - - - - - - - - - - - - agcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgttg