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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatatgaagtgattagcttagttgaagtatcggatgaagcaatttctgccatacaacacttgtatgattgacaagatctccctttcattacttttaacagTGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGACGCCGCTTCCCTTCTCGACACTTCCTTCGAGTGGCGTTGCACAGAGGCCAGTTTCTG

Basic information

species Oryza sativa
transcript LOC_Os06g45820.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45820.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G110408_T01 (Zea mays), 3'ss of exon 1
gatatgaagtgattagcttagttgaagtatcggatgaagcaatttctgccatacaacacttgtatg--------attgacaagatctccctttcattacttttaacagTGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGACGCCGCTTCCCTTCTCGACACTTCCTTCGAGTGGCGTTGCACAGAGGCCAGTTTCTG
   ||||  |    | | |||   |||   | |    |    ||||| |  | ||||| ||||           |||||| ||||||| || ||  |||||||  |||| ||| |||||||| ||| |||||||| | ||||| ||||||  |  ||||||||||||| |||||  ||| ||||| ||| |||| |||||||| || |
--gatgatatag--aacatagaccaagctcctgggtgatttttttcttctttgcaacaattgttcatttcactcattgacgagatctctctctc--tactttt--cagTAAGCAAAGATGGCACCACCATCCATGTGTCTTGCGGCAAAGGGGGTGCTTCCCTTCTCGGCACTTATTTCAAGTGGTGTTACACAAAGGCCAGTGTCAG
















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|88407453|gb|CI586294.1|CI586294
EST:     TCTCCCCTCCACGCCCCGCTCCGATCCACTCAG                         TGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGACGCCGCTT
genomic: TCTCCCCTCCACGCCCCGCTCCGATCCACTCAGgtgcgtgctc ... cttttaacagTGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGACGCCGCTT
EST: gi|88590228|gb|CI709063.1|CI709063
EST:     TCTCCCCTCCACGCCCCGCTCCGATCCANTCAG                         TGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGAAGCCGCTT
genomic: TCTCCCCTCCACGCCCCGCTCCGATCCACTCAGgtgcgtgctc ... cttttaacagTGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGACGCCGCTT
EST: gi|88298775|gb|CI565972.1|CI565972
EST:     TCTCCCCTCCACGCCCCGCTCCGATCCACTCAG                         TGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGACGCCGTTT
genomic: TCTCCCCTCCACGCCCCGCTCCGATCCACTCAGgtgcgtgctc ... cttttaacagTGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGACGCCGCTT
EST: gi|88585160|gb|CI702770.1|CI702770
EST:     TCTCCCCTCCACGCCCCGCTCCGATCCACTCAG                         TGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGACGCCGCTT
genomic: TCTCCCCTCCACGCCCCGCTCCGATCCACTCAGgtgcgtgctc ... cttttaacagTGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGACGCCGCTT
EST: gi|88425698|gb|CI689349.1|CI689349
EST:     TCTCCCCTCCACGCCCCGCTCCGATCCACTCAG                         TGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGACGCCGCTT
genomic: TCTCCCCTCCACGCCCCGCTCCGATCCACTCAGgtgcgtgctc ... cttttaacagTGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGACGCCGCTT
EST: gi|38474786|gb|CF958919.1|CF958919
EST:     CTCTCCCCTCCACGCCCCGGGCCGATCCACTCAG                         TGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGACGCCGCTT
genomic: CTCTCCCCTCCACGCCCCGCTCCGATCCACTCAGgtgcgtgctc ... cttttaacagTGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGACGCCGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgccatacaacacttgtatgattgacaagatctccctttcattacttttaacagTGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGACGCCGCTTCCCTTCTCGACACTTCCTTCGAGTGGCGTTGCACAGAGGCCAGTTTCTG
                    gattgac  putative branch site (score: 3)
                               tctccctttcattact  putative PPT
                                     tttcattacttttaa  TA-rich tract