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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtgtagtagttcctacaacatgctctatctgtttaagattctatctttctgtttcttaccatatgatgaaagttctaatccattccatggctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAATTGACCTGTGTGGTCTTCACGTAAGCGAGGCGATACACGCCCTGAACTAT

Basic information

species Oryza sativa
transcript LOC_Os03g08270.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g08270.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G830874_T04 (Zea mays), 3'ss of exon 4
-ggtgtagtagttcctacaacatgctctatc-tgtttaagattctatctttctgtttcttaccatatgatgaaagttctaatccattccatggctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAATTGACCTGTGTGGTCTTCACGTAAGCGAGGCGATACACGCCCTGAACTAT
     | ||  |      || |  ||  | | || ||  | || |   | |  | |  |||  |    |||||||  |||||  ||| | ||     | |||||| ||||  ||| |||| ||||||||  | |||||||||||| ||||||| || || |||||||||||| | |||||||| ||||||| ||||||||| 
taagtttgtgatggtaggaagaccctgcaacatgatttcgtttatccatatgagatgtttagtactacatgaaag--ctaatatattgcctgttcccaacagATTACAAACACCACAATTGCAAGGCCTCATCCAGGAGCAAAATCCCCCAATCGATCTCTGTGGTCTTCACATCAGCGAGGCAATACACGTCCTGAACTAC

upper sequence: LOC_Os03g08270.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G017254_T02 (Zea mays), 3'ss of exon 6
ggtgtagtagttcctacaacatgctctatctgtttaagattctatctttctgtttcttaccatatgatgaaagttctaatccattccatggctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAATTGACCTGTGTGGTCTTCACGTAAGCGAGGCGATACACGCCCTGAACTAT
     |||  ||   ||  |    |  |       | |    ||  ||| || |       |         |   |||||  |||   ||   | | |||||| ||||| |||||  ||||||||||  | |||||||| ||| ||||||| || || |||||||||||| | |||||||| || |||| ||||||||| 
aaaacagtgttttgcacggctatatgcacgatagcacggccttaaatttgtgatgggaggaaggctgcatgaaagctaatatattgtctgttctcaacagATTCCAAATACCAGAGCTTCAAGGCCTCATCCAGGAGCAGAATCCCCCAATCGATCTCTGTGGTCTTCACATCAGCGAGGCCATGCACGTCCTGAACTAC
















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|86429806|gb|CI082229.1|CI082229
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|88845205|gb|CI084130.1|CI084130
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|4715235|gb|AU056352.1|AU056352
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|88847048|gb|CI001320.1|CI001320
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|88265557|gb|CI376459.1|CI376459
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|44670645|gb|CR284079.1|CR284079
EST:     TGGCAAACCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|66921841|gb|CX108689.1|CX108689
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|88969239|gb|CI382788.1|CI382788
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|88441892|gb|CI557545.1|CI557545
EST:     CTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: CTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|86260890|gb|CI066565.1|CI066565
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|86908615|gb|CI318954.1|CI318954
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAAGTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|29615641|gb|CB620653.1|CB620653
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|86884922|gb|CI314498.1|CI314498
EST:     GCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: GCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctgtttcttaccatatgatgaaagttctaatccattccatggctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAATTGACCTGTGTGGTCTTCACGTAAGCGAGGCGATACACGCCCTGAACTAT
                            ttctaat  putative branch site (score: 2)
                                              ctttacc  putative PPT
       tttctta  TA-rich tract