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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaacaattctttacaaagagcaataatttgttatcattcaggcaccatgaaacttaactgacttatttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT

Basic information

species Oryza sativa
transcript LOC_Os04g58580.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58580.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 8
gtacaaacaattctttacaaagagcaataatttgttatcattcaggca-----------ccatgaaacttaactgacttatttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT
||| |||   |    || ||      |   ||| |||  |     | |           | |||  ||| ||     | |||| ||  |||| |||||||| || ||||||||||| |||||||||||||||||||| || ||| ||||||||||||||||||| |||||||||||||||||||||
gtataaattgtgtactaaaagtcagtaccttttcttagtaggagaggatggaataaaatctatgggactgaaacagttgatttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT

upper sequence: LOC_Os04g58580.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 8
-------------------------gtacaaacaattctttacaaagagcaataatttgttatcattcaggcaccatg--aaacttaactgacttatttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT
                          | |     | | || || |     | | |  |||||    |        |||  |||  |     | |||  | ||  |||| || || || || || |||||||| || || |||||||| ||||| || ||  | ||||||||||| || |||||||| ||||| |||||||| 
ggttatgtattttggtttttatcacattctctagaattttcactatccatattgaaatgttaggcgtataattttatgctaaaagtttgcaatttaagttct-caGGTTCACAATATACGCCCGAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGA-

upper sequence: LOC_Os04g58580.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA09G39800.1 (Glycine max), 3'ss of exon 8
------------------------gtacaaacaattctttacaaagagcaataatttgttatcattcaggc---accatgaaacttaactgacttatttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT
                         | |     | | || || |     | | |  |||||    |    |   ||| | ||| ||  |  | |||  | ||  |||| || ||||| || || |||||||| || || |||||||| ||||| || ||  | ||||||||||| || |||||||| ||||| |||||||||
gttatgtattttggtttttatcatattctctagaattttcactatccatattgaaatgttaggtgtataactttaccctaaaagtttgc-aatttaagttct-cagGTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGAT

upper sequence: LOC_Os04g58580.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv15s0046g03520.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------gtacaaacaattctttacaaagagcaataatttgttatcattcag--------gcaccatgaaact--taac-tgacttat--ttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT
                                 | ||   ||||| | |       ||||||| ||| |   |||  |        ||| | ||||||    |||   | ||||  | |    || | || ||||| || || || ||||| || ||||||||||| ||||| || ||| | ||| ||||||||||||||||||| || || || ||||||
gtataaacttcagatccttcgaagcaaaagattgaactgtcaatt-tgtgtttgtggcaataaattgattgtatttggataaacatgcatcctgaaacaaacaacacaatttataatcatatcagATTCACAACATACGTCCGAAGATGGTTTCTGTGCTTCGTGAGAAGTTTGCTCACCTAAACCTGACATTTTCTATTGGAGGACAAATAAGCTTTGAT

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|29627056|gb|CB632067.1|CB632067
EST:     GGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAG                         GTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCC
genomic: GGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAGgtacaaacaa ... tttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCC
EST: gi|58604165|gb|CK014693.1|CK014693
EST:     GGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAG                         GTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCC
genomic: GGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAGgtacaaacaa ... tttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCC
EST: gi|29641676|gb|CB646683.1|CB646683
EST:     GGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAG                         GTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCC
genomic: GGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAGgtacaaacaa ... tttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCC
EST: gi|86547064|gb|CI187270.1|CI187270
EST:     GGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAG                         GTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCC
genomic: GGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAGgtacaaacaa ... tttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCC
EST: gi|88846893|gb|CI005872.1|CI005872
EST:     GGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAG                         GTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCC
genomic: GGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAGgtacaaacaa ... tttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCC
EST: gi|8859293|gb|AU096611.1|AU096611
EST:     GGAGAAATTGTAGTCAAGAAGANCGTGATGAGTTTGAAAAGTATGATAAG                         GTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCC
genomic: GGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAGgtacaaacaa ... tttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCC
EST: gi|86542297|gb|CI182503.1|CI182503
EST:     GGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAG                         GTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCC
genomic: GGAGAAATTGTAGTCAAGAAGAACGTGATGAGTTTGAAAAGTATGATAAGgtacaaacaa ... tttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caataatttgttatcattcaggcaccatgaaacttaactgacttatttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT
                                   aactgac  putative branch site (score: 2)
                                         cttattt  CT-rich tract
                                        acttatttactata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaaacaattctttacaaagagcaataatttgttatcattcaggcaccatgaaacttaactgacttatttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT