Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcagctcacagataccattatcaggccttcctgcatttccttttctaccactgatgctcatgtttcttaacctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATC

Basic information

species Oryza sativa
transcript LOC_Os06g43860.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G055243_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------------gtatgtcagctcacagataccattatcaggccttcctgcatttccttttctacc-actgatgctcatgtt-tctta----acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATC
                                                      | || | |   |   ||   |||           |   ||   || || |||   ||| |||   || || || |     || | | |||||||| |||||||||||  ||||||||||||||||| | ||||| || ||||||||||| |||||||||||||| ||||| ||||||||||||| |||| 
gtaagtgaacacattgatcctatcactcccagcaccattcctagttactcatgagcatattattacgttgaacacatggatcctatcactcccagcaccattcctatttactcatgagtatattatcgtggaccacttgtttagGAGGAAGACAAGGCTCGACTGGTGCAGGAAACAGGGCTACAACTGAAGCAGATCAATAACTGGTTTATCAACCAGCGTAAGCGGAACTGGCACAACAATT

upper sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 5
---gtatgtcagctcacagataccattatcaggccttcctgcatttccttttctaccactgatg--------ctca-----tgtttcttaacctttat--agGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATC
    ||   ||  |   || |||    |  ||   ||     |||  | |||  |  | | ||         ||||     ||||  | ||  ||| |  |||||||||| ||||| || |||||||||||||| || ||||| ||||| ||||||||||||||||||||||| ||| | ||  |||||||||| ||||| |
aagctactccaaattgaagctact-ccaggagaattttaca-attgacattttgaagattaataaatgctgtctcacaatttgttcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC

upper sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G06890.2 (Glycine max), 3'ss of exon 4
-----------gtatgtcagctcacagatacc-attatcaggccttcctgcatttccttttctaccactgat----gctcatgtttcttaacctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATC
           ||| |  |   || |   |   |  |   | | ||     | ||  | ||  |  | |  |      | ||  |||      |||  |||||||||| ||||| || |||||||||||||| || |||||  |||| ||||||||||||||||||||||| ||| | ||  |||||||||| |||| ||
aaatgaacatagtaagctactacagaagaatttaacaattgactttttcaaaattaatattaaatgatttctcacaatttattcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGTTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAGTC

upper sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA14G13750.2 (Glycine max), 3'ss of exon 4
----gtatg-tcagctcacagataccattatcaggccttcc--------tgcatttccttttctaccactgatgctcatgtt---tcttaacctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATC
       ||  |   | | ||  |  |||||| |   | ||          ||| ||| ||   |    |  | || |  |    || |   |||   |||||||||| |||||  | |||||||||||||| || |||||| |||| ||||| ||||||||||||||||| ||| | ||  |||| |||||||||||||
tatcaagtgacctttttaaagtaaatattatctgctatcccacacaagccacatctcccttatcaatctttttactgaactcaaatcatgttcttgtcagGAGGAGGATAAGGCAAGGTTGGTGCAGGAAACTGGATTGCAATTAAAGCAGATTAATAATTGGTTTATCAATCAAAGGAAGAGGAATTGGCACAGCAATC

upper sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G32980.2 (Glycine max), 3'ss of exon 4
---gtatgtcagctca--cagataccattatcaggccttcc--------tgcatttccttttctaccactgatgctcatgtt---tcttaacctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATC
   || |      | |   | |||  | |||| |   |  |          |||   | ||   |    |  |||| |  |    || |    |||  |||| ||||| |||||  | |||||||| ||||| ||||||||| |||| ||||| ||||| ||||||||||| ||| | ||  |||| |||||||||||||
atggtcttctttttaaagtaaatattactatctgctatctcacaccggccacatcgtccttatcaatctttttgctgaactaaaatcatgttgttttcagGAAGAGGATAAGGCAAGGTTGGTGCAAGAAACTGGGTTGCAATTAAAGCAGATTAATAACTGGTTTATCAATCAAAGGAAGAGGAATTGGCACAGCAATC

upper sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S154_83V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------gtatgtcagctcaca-gataccattatcaggccttcctgcatttccttttctaccactgatgctcatgtttcttaacctttat----------------agGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATC
                                                     | |   || ||||   ||  ||  ||      |   |  || |   |   ||    |||    |   ||| |  |||| | |                ||||||| || ||||  ||  || | ||||| ||||| ||| || | || ||  | ||||||||||| || |||||||| || |||||||||||||||||||
gtatcaaaaaattcatcaggaatcctgaactacgtatatccattcatgctttatgttctagttcacgtaatttcagaattccatttatatatatatatatacgtattggtgacatgctgatttttccacctctgttttgcactcctcaaccagGAGGATGAAAAGGAGCGGCTGATTCAGGAGACAGGTTTGGAATTGAAGCAAGTGAATAATTGGTTCATAAACCAACGCAAGCGGAACTGGCACAGCAATC

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|87008402|gb|CI301160.1|CI301160
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29638818|gb|CB643827.1|CB643827
EST:     TTACTTTGAAAGCATGGTGGCAGGCTCACTTTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|23514961|gb|BU673870.1|BU673870
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29679811|gb|CB676086.1|CB676086
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|38565817|gb|CK085270.1|CK085270
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29663219|gb|CB659494.1|CB659494
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|38475492|gb|CF959625.1|CF959625
EST:     GGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: GGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29645298|gb|CB650305.1|CB650305
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|38565678|gb|CK085131.1|CK085131
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29657867|gb|CB654142.1|CB654142
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29659496|gb|CB655771.1|CB655771
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|58693265|gb|CK081952.1|CK081952
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29645222|gb|CB650229.1|CB650229
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29637144|gb|CB642153.1|CB642153
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29657258|gb|CB653533.1|CB653533
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|31818558|gb|CD645554.1|CD645554
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29669194|gb|CB665469.1|CB665469
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29645255|gb|CB650262.1|CB650262
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|87011013|gb|CI286088.1|CI286088
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29667364|gb|CB663639.1|CB663639
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCTAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|29667365|gb|CB663640.1|CB663640
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCTAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|109974476|gb|DT806929.1|DT806929
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG
EST: gi|58695467|gb|CK084154.1|CK084154
EST:     CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACT                         GAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAGCAG
genomic: CTACTTTGAAAGCATGGTGGCAGGCTCACTCTAAATGGCCATACCCAACTgtatgtcagc ... acctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccttcctgcatttccttttctaccactgatgctcatgtttcttaacctttatagGAGGAGGACAAGGCTCGCTTGGTGCAGGAAACAGGGTTGCAACTAAAACAGATCAATAATTGGTTTATCAACCAACGTAAACGGAACTGGCACAGCAATC
                                        tcttaac  putative branch site (score: 2)
                                              cctttat  CT-rich tract
                                      tttcttaa  TA-rich tract