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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcatcaggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA

Basic information

species Oryza sativa
transcript LOC_Os02g54340.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 6
gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcatcaggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
             | |    | | | |  ||| | |||  | || || ||| |   |||||||   |||||||||  ||   || |||| |   |||| | ||||   | |   || ||   |||||||||| ||||| |||||||||||||| |||||||||||||||||||||||||||||||| || ||||||||||||||||| ||||| |||||||| |
------------gtatgtgatccttttttcttcttgtg--agctggcacatac---tgcatca---tagttagttacgggactagtttggt---tactctgtgct---tgtaccttttttgcagGTTGTTGAACTTCCTATGCTTCACCCAGAAAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAAGGCGTCCTTTGCTATGGCCCACCTGGCACTGGCAAGA

upper sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 6
gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcat-caggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
      |||    ||   |||||   ||  || |      ||  || | ||  ||| | || || | ||  | |   |  | |||||||  ||| |  | | |||||                 ||||||||||||||||||||| ||||||||||| || || ||||| || ||||||||||||||||| || ||||||||||| || || || ||||||||||
-----gtaagtgattggaagttcccttcattttt------aatctgtt-ataattgaggatgcaagttacatggcgcta-atttatttttttatattttatctgcta-----------------gGTTGTTGAGCTTCCCATGCTCCACCCAGAGAAATTCGTTAAGCTAGGAATTGATCCTCCAAAGGGTGTTCTTTGCTATGGTCCACCAGGGACTGGCAAAA

upper sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 6
gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcat-caggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
            ||  | | |  |  | || |    |   ||  || | ||  ||| | ||  | | ||  | ||  |    ||||||   ||| |  | | |||||                 ||||||||||||||||||||| ||||| ||||| || || ||||| || ||||||||||||||||| || ||||||||||| || || || ||||||||||
-----------gttagtgattggaagttcccttgatttttaatctgtt-ataattgcggatgtaagttacatggtgctaattttatttatttatattttatctgcta-----------------gGTTGTTGAGCTTCCCATGCTCCACCCTGAGAAATTCGTTAAGCTAGGAATTGATCCTCCAAAGGGTGTTCTTTGCTATGGTCCACCAGGGACTGGCAAAA

upper sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 6
gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcatcaggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
                                     | ||  |   |     || | | |        ||  |  || | |   |  |  |  |     |   |  | |||  |   |   |||||||||| |||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| || ||||| |||||||| || |||||||| ||||
-------------------------------------gtaag-tcattggaatttttacttattttacatttataatgaagtagataagtcacgtgtcactaatttgtaatt--tcactgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGCCCCCCAGGAACTGGGAAAA

upper sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 6
gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtgcatcaggctagttagttttggacttattttgctatt-tactgtttgctaattattgtttgttcata-gGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
                                             |    || |||    |     ||  |    ||  | | ||  ||   || | | |      | || |  |||      | ||||||||| |||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| || ||||| ||||| || || |||||||| ||||
---------------------------------------------gtaagtcattgaaatttcacttatcttacattataatgataatgaagttatgcggcactaaatttgtcatttccctgcaagGTTGTTGAACTTCCCATGCTTCATCCAGAGAAATTTGTCAAGCTTGGGATTGATCCTCCAAAGGGTGTTCTTTGTTATGGTCCCCCAGGAACTGGGAAAA

upper sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 6
---------gtatactaatcttttttcagttcatatcccttgt-cgtgcaaacttgctcatccttgtgcatcaggctagtt---agttttggacttattttgctatttactgtttgctaattattgt----ttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
          | |  | |  ||||||    ||| |||   | | | |  | ||    || | ||||   | ||| ||||||     |  ||      | |  |  | |  |||||||| ||  || |    |||    ||||| |||||||| || ||||| ||||| ||||||||||| |||||||| ||||||||||| ||||| || || |||||||| ||||||||||| || ||||
gtgtgtatattctttttacatttttttttgtcagatcatatatgcatttacaccgtgtctttcttgattaacag-ctagtttttgatcctgtgaacttctgtccttctcttgtttgctgatatttataactttggctctagGTGGTTGAGCTCCCTATGCTCCACCCTGAGAAGTTTGTGAAGCTTGGAATTGATCCTCCTAAGGGTGTTCTCTGCTATGGTCCTCCTGGAACCGGTAAAA

upper sequence: LOC_Os02g54340.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatactaatcttttttcagttcatatcccttgtcgtgcaaacttgctcatccttgtg-catcaggctagttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
                   | | || |          ||    ||         |||| || || ||  ||| |||||  |  | |  || ||  |  |  ||  |  || |  |      |||||| || ||| | || ||| | || || |||||||| || ||  | || |||||||| || || || |||||||||||||||||||| ||||||||||| |
-------------------gctgatgtggtaaagatagctgtttttaaaggtagtgtggcaacaagcccgttggttttaaaggtgt--tgatacatggtaattcgtggttgtactg----aatagGTGGTGGAGTTGCCAATGTTGCATCCTGAGAAGTTCGTGAAATTGGGAATTGATCCGCCCAAAGGAGTCCTTTGCTATGGCCCTCCCGGAACTGGCAAGA

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|29684844|gb|CB681119.1|CB681119
EST:     CATATAATGATGTGGGTGGTTGCAAGGAACAGATTGAAAAAATGCGGGAG                         GTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATT
genomic: CATATAATGATGTGGGTGGTTGCAAGGAACAGATTGAAAAAATGCGGGAGgtatactaat ... ttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATT
EST: gi|58685776|gb|CK074463.1|CK074463
EST:     CATATAATGATGTGGGTGGTTGCAAGGAACAGATTGAAAAAATGCGGGAG                         GTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATT
genomic: CATATAATGATGTGGGTGGTTGCAAGGAACAGATTGAAAAAATGCGGGAGgtatactaat ... ttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATT
EST: gi|58600395|gb|CK010923.1|CK010923
EST:     GATTGAAAAAATGCGGGAG                         GTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATT
genomic: GATTGAAAAAATGCGGGAGgtatactaat ... ttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagttttggacttattttgctatttactgtttgctaattattgtttgttcatagGTTGTTGAGCTTCCCATGCTTCACCCAGAGAAGTTTGTCAAGCTTGGTATTGATCCTCCAAAGGGGGTCCTTTGCTATGGCCCTCCTGGAACTGGCAAAA
                                tgctaat  putative branch site (score: 2)
                                            tttgttc  putative PPT
            ttattttgctattta  TA-rich tract