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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcatgctaattatcatggtctgttttttttatttggtctcttgtttcttttttccacttgtttcacaaacatagttctgatcaccatttattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT

Basic information

species Oryza sativa
transcript LOC_Os07g47530.1
intron # 21
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 21
lower sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
tagcatgctaattatcatggtctgttttttttatttggtctcttgtttctttttt--ccacttgtttcacaaacat-agttctgatcaccatttattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT
 ||     ||||| ||   ||       |     | |     | |  |  | ||   |||   |  |   || |||  |||||||||| | | | | | |||||||||||| || |||||||||||||| |||||||| || || |||||||||||||| ||||||||||||||||||||||| || ||||||||||||||||
-agtg-attaattgtccgagtaaccgactaggggtcgactagtcgcctggtcttcgaccaggcgacttgaaatcattggttctgatcatc-tatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 17
---tagcatgctaattatcatggtctgttttttttatttggtctcttgtttctt----ttttccacttgtttcacaaacatagttctgatcaccatttattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT
    |  ||  | ||| |  | || |   |   || |        |||||   |      | |||  ||| |  ||  | || || | || ||  |||    |  |||| || || |||||||||||||||||||| ||||| || || || || |||||||| || ||||| ||||| || ||||| || |||||||| ||||| |
gtgaaagattttcattttagttgtttaaatgacttgtgaaagaaattgttgagtagatcatgccatgtgtgtagca--cctaattgtaattac--tttgggtat-agCCTTGCAAAGGAATATTGCTTTTTGGCCCTCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
--tagcatgctaattatcatggtctgttttttttatttggtctcttgtttctttt------ttccacttgtttcacaaacatagt-tctgatcaccatttattcac---cagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT
  | | |   |  || |  |    || |||   |     ||        | ||||      |   | |  | |||      |||   || ||    |||  ||       |||| || |||||||||||||||||||| || ||||| || || || || |||||||| || ||||| ||||| || ||||| || ||||| || ||||| |
gttggtagatt--ttctttttagttgctttaaatgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
-----tagcatgctaattatcatggtctgttttttttatttggtctcttgtttctt----ttttccacttgtttcacaaacatagttctgatcaccatttattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT
      |  ||  | ||| |  | || |   |   || |        |||||   |      | |||   || |  ||  | || || | || ||  |||    |  |||| || ||||||||||||||||||||||| ||||| || || || || |||||||| || ||||| ||||| || ||||| || |||||||| ||||| |
gtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagca--cctaattgtaattac--tttgggtat-agCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 16
-----tagcatgctaattatcatggtctgttttttttatttggtctcttgtttcttttttc-cacttgtttcacaaacatagt-tctgatcaccatttattcac---cagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT
     |||  |     ||    || | |   |   || |        || |||  |   ||  | | |  |||      |||   || ||    |||  ||       |||| || |||||||||||||||||||| || ||||| || || || || |||||||| || ||||| ||||| || ||||| || ||||| || ||||| |
gttgatagattttctttttagttgctttaaatgacttgtggaacacattttttagtagatcatattcgaatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 21
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
tagcatgctaattatcatggtctgttttttttatttggtctcttgtttcttttttccacttgtttcacaaacatagttctgatcaccatttattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT
     | |   ||||     |  |  ||| ||  || ||    |||| ||  |    |  ||   | ||||||||  | ||||     |||| |   |||||    || || ||| || | ||||| || |||||||| || ||||| ||||| || ||||| || ||||| ||||||||||| ||||| ||||| || |
----gtaccttttattgctatacggatttatttgttagt----tgttactcctacataactgaaac-caaacatatatttgat----gtttaat--gcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 21
lower sequence: AT1G02890.2 (Arabidopsis thaliana), 3'ss of exon 20
tagcatgctaattatcatggtctgttttttttatttggtctcttgtttcttttttccacttgtttcacaaacatagttctgatcaccatttatt-cac-cagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT
            || | |  | || |||||  | |       |||||||    ||| |  |  |    ||||  | || | |      ||| || ||  |||||    ||||| ||| |  | ||||| || ||||||||||||||||| ||||| || |||||||| ||||| |||||||| || || |||||||| || |
-----------gtacctttct-tgctttttaaaatcaaatcgttgtttca---ttcaatattctatggaaactgaattataactgttttttttttcatgcagCCTACAAAGGGTATACTATTGTTTGGACCGCCTGGTACGGGGAAGACAATGCTGGCAAAAGCTGTAGCAACCGAGGCTGGGGCAAACTTTATCAATATTT

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 21
lower sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
tagcatgctaattatcatggtctgttttttttatttggtctcttgtttcttttttccacttgtttcacaaacatagttctgatcaccatttattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT
                             | | | || | | || |||  |||||    |||| | || ||                 |||||    ||||| |||| |||  || |  | ||||| || || || || || ||||||||||||||||| || ||||| ||||||||||| || ||||| ||||| || |
----------------------------gtctgtgtg-tttgttatttgctttttttctttgtctaacgaa-----------------tttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

upper sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 21
lower sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 10
tagcatgctaattatcatggtctgttttttttatttggtctcttgtttcttttttccacttgtttcacaaacatagttctgatcaccatttattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT
                             | | | || | | || |||  |||||    |||| | || ||                 | |||    ||||| |||| |||  || |  | ||||| || || || || || ||||||||||||||||| || ||||| ||||||||||| || ||||| ||||| || |
----------------------------gtctgtgtg-tttgttatttgctttttttctttgtctaacgaa-----------------tctatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

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:     TGCTTCCGTTGCAAAGGCCCGAATTGTTCTCCAAAGGACAACTTATGAAG                         CCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATG
genomic: TGCTTCCGTTGCAAAGGCCCGAATTGTTCTCCAAAGGACAACTTATGAAGgtagctcaag ... tattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATG
EST: gi|58688870|gb|CK077557.1|CK077557
EST:     TGCTTCCGTTGCAAAGGCCCGAATTGTTCTCCAAAGGACAACTTATGAAG                         CCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATG
genomic: TGCTTCCGTTGCAAAGGCCCGAATTGTTCTCCAAAGGACAACTTATGAAGgtagctcaag ... tattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATG
EST: gi|29669556|gb|CB665831.1|CB665831
EST:     TGCTTCCGTTGCAAAGGCCCGAATTGTTCTCCAAAGGACAACTTATGAAG                         CCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATG
genomic: TGCTTCCGTTGCAAAGGCCCGAATTGTTCTCCAAAGGACAACTTATGAAGgtagctcaag ... tattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttttttccacttgtttcacaaacatagttctgatcaccatttattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT
                               ttctgat  putative branch site (score: 3)
                                           tttattc  putative PPT
                                          atttattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcatgctaattatcatggtctgttttttttatttggtctcttgtttcttttttccacttgtttcacaaacatagttctgatcaccatttattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
-agcatgc
- - - - - - - -catggtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgat