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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA

Basic information

species Oryza sativa
transcript LOC_Os07g47180.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
--gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatcc-----------gccacaatcagaaacatact--cctagaacaatgttaagctcacagctc-------actcgatcgtacaactt---------gcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
   ||||  ||  |   | ||||||||| || |   ||||||| |||||| |             ||    |  | | |||     ||| ||    ||  ||  |  |  |||       || ||||  |    |||          |||||||||||  | ||||| ||||||||||| ||||||||||| |||||||||||||| || |||||||| ||||| || || | ||| ||||| ||||| |
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgcatataccgtgttgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA

upper sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G873277_T01 (Zea mays), 3'ss of exon 6
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatga-----tccgc-cacaatcagaaacatact-cctagaacaatgttaag------ctcacagctcactcgatcgtacaactt-------------gcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
|| | ||  | |   | |||| |||| || |   ||||||| ||||||     |  ||  | | |  |   | ||    || |||   ||  ||       |||   ||| || | ||  | || |||              |||||||||||  ||||||| ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| ||| ||||| ||||| |
gtacattcctatattt-atttgagttacttagcagttcattggcatgaactcgtttgcatatactgtgttgcgtatcatctggaagggtgccaaatcttgtctcttggctaacacaattcttcatcttttctctcttatctacagAAAAGAAGGTTAATAACTCATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCGCATCAGGATGGCGCACTTGGATTTCCCTTGGGCTGTTCGA

upper sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G10470.1 (Glycine max), 3'ss of exon 6
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
    | |    | |  || ||   | |   ||      ||     || |     |||         || |   ||||||| ||||||  |  ||||||   |            |||||| | || | || || |||||| ||||||| |||||||||||||| ||||| ||||| || || || ||||| || || || ||||||||||||| |||| 
--attctccccttgtggaattttttgggctatccaag-ataattgtgttatattacagct---tctattcgtatagaacagtgttaatgtt-cagctcttac------------tgcagAGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC

upper sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G38140.1 (Glycine max), 3'ss of exon 6
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgat-ccgccacaatcagaaacatactcctagaac--aatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
                   |  |  |    || | |  || | ||||     |   ||      | | ||||  ||   |  ||| ||    | |  | |   |   || ||    || |||| | |  ||||  |||||||||||||||| ||||||||||| || ||||| ||||| || ||| | |||||  | || || ||||||||||||| |||| 
------------------atatatatatatatatatatatatacatggggttggttcatatctcagcttacttttatgtcttaatcttgtagtaatggttgcttaactctta----ttacagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTTCCTCCTCCTCATGAAGATGGAACTCTAGGCTATCCTTTGGGTTCTTCAC

upper sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 6
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
||   || |    |   ||||  |  | | ||      ||     || |     |||        | || |  ||||||| ||||||  |  ||||||   |            |||||| | |  | || || |||||||||||||| |||||||||||||| ||||| ||||| || || || ||||| || || || ||||||||||||| |||| 
gtatattctacgtggaaattttgg--ggttatccaag-ataattgtgttatattacagctttt--cttagtg-tagaacagtgttaatgtt-cagctcttac------------tgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC

upper sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 6
------------------------------------------gtgcttttttttggctgatttcagttgctcat-ttgttcatttgcatgatccgccacaatcagaaacatactcctagaac-aatgttaagctcacagctcact----cgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
                                           ||||| | |    || ||   | |   |  | || || ||       |  |   | |||    |    |    || ||  |||||| |  | | |  |  ||     |||   |    |  |||| |||  |  |||| || ||||||||||| |||||||||||||||||||| ||||| |||||| | |||||    ||||| | ||||||||| | ||| |
gtatgttaaagaaatttacttctattgtttgatgcctttgtactgcttctatccttctaataaaattcatttttgttttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttga--ttaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA

upper sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G40330.1 (Glycine max), 3'ss of exon 6
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
              |||||||   || |          || ||||||||      ||  |||  | | ||||  |    ||  ||||  |     ||     |||        |  |||| |||| | ||||| || ||||||||||| |||||||||||||||||||||||||| |||||||| |||||   | |||| | ||||||||| | |||| 
-------------actgatttattttacaatacaaagtatctgcatgat--aatgcatccagtcaaa-actcaaaagtaaagattaaatttgttacta---tgatttcttctgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTCCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTGGGATCTTCAC

upper sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagct--cact-cgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
                   |||   ||  |  || ||   || ||  |      | |  ||  || || |  | ||   || || ||| | | |  |   |||  |||        |  |||| |||| | ||||| || ||||||||||| ||||||||||| |||||||| ||||| |||||||| |||||   | |||| | |||||| || | |||| 
-------------------ttctaatgaactcttatt---ttacaatagaaagtatatgcatgaatatgcatccagtcaaaagtaaagattaaatttgttactatgatttcttgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC

upper sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
          |    ||   ||| |     || | | |||     || | |   | |     |   |   |  |     ||| ||    | |  | | |     || ||    || |||| | |  ||||  |||| ||||||||||| |||||||||||||| ||||| ||||| || ||  | |||||  | ||||| ||||||||||||| |||| 
--------cataaagtggcatcaat-atatatatatacatggagttggttc---atatctcaacttacttttatgtcttaatattgtagtaatggttta---actctta----ttacagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC

upper sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G30030.1 (Glycine max), 3'ss of exon 6
------------------------------------------gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaac-aatgttaagctcacagctcact----cgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
                                           ||||  |||    || ||   | |   |    | || |||      |  |   | | |    |    |    || ||| || ||| |  | | |  |  ||     |||   |    |  |||| |||  |  |||| || ||||||||||| |||||||||||||||||||||||||| |||||| | |||||    ||||| | ||||||||| | ||| |
gtatgttaaagaaatttacttctattgttttatgcctttgaactgctgctttccttctaataaaattcattatcatttttattattgaaaatctgtatagttgtgattgaaagtataaaactaacgttga--ttaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTCCCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA

upper sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaac-atactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
     |||  |    ||  | ||  |  |  |||||| ||     || | |   | | |   |     ||    | ||    |||    || | | |||   |  |  || |     ||||   || | |||||||| ||||||||||| |||||||||||||||||||| ||||| ||||| ||||||||  | ||||| || || ||||||| |||| 
-----tttcatcatgtggctccatataat--tttgttgatcaagttggttc-tgatacttgtagtttgtagattttgattgctgt----cttatatctc---catttctaaa-----cagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC

upper sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 9
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
       ||    |||  | |   ||  | || | | || |  |  ||  |    ||| ||||     | |  | |||   ||||   |      ||  ||  |            |||  |||| | |||||  | ||||||||||| ||||| |||||||||||||| ||||| || || ||||| || ||| |||| |  || ||||||  |||| 
-------ttgagagcttttgtttcttttttatgtttgcaatcacccgagtccttgcaaccagagttcgattgtttgaatt-tgttttccgtgtttctttctgaa-----------acagCGAAGACGCCTAATCTCCCATGCAAATGCAAAGAGTAAGAGTGAAAAGTTTCCTCCACCTCACCAGGACGGAGCAGTTGGCTTCCCCTTGGGTGCTTCAC

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|22306085|gb|BQ907307.1|BQ907307
EST:     TTCCAGCACCGGGAAGCAAATGCTGAGCTTCATAGCAAATATTG-TATAT                         ATAAGTAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTT
genomic: TTCCAGCACC-GGAAGCAAATGCTGAGCTTCA-AGCAAATATTGATGTATgtgctttttt ... caacttgcagAAAAG-AAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTT
EST: gi|86497666|gb|CI140299.1|CI140299
EST:     TGTTCCAGCACCGGAAGCAAATGCTGAGCTTCAAGCAAATATTGAT--A-                         AAA-GAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTC
genomic: TGTTCCAGCACCGGAAGCAAATGCTGAGCTTCAAGCAAATATTGATGTATgtgctttttt ... caacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
                             agctcac  putative branch site (score: 3)
               aatgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagctcactcgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG