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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgttattgcttttcttacatgaacttgccaaagtacaaatacagaataatcaactaaggtttcctttccacaatctcaccatgttatgaatttgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAATGGTCTGTAGATAAGGTTCTTGAGGTTATTAACAAAAACTGCCGTTCAT

Basic information

species Oryza sativa
transcript LOC_Os01g56630.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56630.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G078576_T04 (Zea mays), 3'ss of exon 14
gtatgtgttattgcttttcttacatgaacttgccaaagtacaaatacagaataatcaactaaggtttcctttccacaatctcaccatgttatgaatttgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAATGGTCTGTAGATAAGGTTCTTGAGGTTATTAACAAAAACTGCCGTTCAT
|||||||||||||  ||| || ||   ||||       || || |||| | ||||| |      |||||        |||  |  || || ||| |  |||||  |||| |||||||||||||||||||||||||||||||| || |||||||| |||||||| || ||||| || ||||| || || || ||||  ||||||||||
gtatgtgttattg--tttattgca---acttt------tataagtacacattaatctat-----tttccagattctcatcatattatattctgagt--gtctgatagGTATTGGATTTCTTCAATAGTCGAATGGACATGCAACAATTAGATGGGGAATGGTCCGTGGATAAAGTGCTTGAAGTCATCAATAAAACTTGCCGTTCAT

upper sequence: LOC_Os01g56630.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G079389_T01 (Zea mays), 3'ss of exon 14
gtatgtgttattgcttttcttacatgaacttgccaaagtacaaatacagaataatcaactaaggtttcctttccacaatctcaccatgttatgaatttgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAATGGTCTGTAGATAAGGTTCTTGAGGTTATTAACAAAAACTGCCGTTCAT
   | |||||  | || |||  | ||| ||| |  |||||||    ||     ||   | |   | || |   |||| | |    ||| || || |  || ||  |||| ||||||||||||||||| |||||||||||||| || |||||||| ||||||||||| |||||||| ||||| || || |||||||  ||||||||||
--gtatgttaccgattatctctcgtgatctttcagaagtaca----caattctattttccagattctcat---cacattgt----atgctacgagt--gtttgatagGTATTGGATTTCTTCAATAGCCGAATGGACATGCAACAATTAGATGGGGAATGGTCTGTGGATAAGGTGCTTGAAGTCATCAACAAAACTTGCCGTTCAT
















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|426809|gb|D22882.1|D22882
EST:     CATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACA                         GTGTTGGATTTCTTCAATAGTCGAATGGNCATGCAGCAGTTAGATGGNGAA
genomic: CATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACAgtatgtgtta ... tgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
EST: gi|58678344|gb|CK067031.1|CK067031
EST:     CATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACA                         GTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
genomic: CATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACAgtatgtgtta ... tgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
EST: gi|5004229|gb|AU069378.1|AU069378
EST:     GAGAATATTTACACA                         GTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
genomic: GAGAATATTTACACAgtatgtgtta ... tgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
EST: gi|29639051|gb|CB644060.1|CB644060
EST:     CATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACA                         GTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
genomic: CATTCAAAAACCATCCCCGCTTCAATGAATTGCTTGAGAATATTTACACAgtatgtgtta ... tgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
EST: gi|5004218|gb|AU069367.1|AU069367
EST:     GAGAATATTTACACA                         GTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
genomic: GAGAATATTTACACAgtatgtgtta ... tgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
EST: gi|86497820|gb|CI140453.1|CI140453
EST:     TCAATGAATTGCTTGAGAATATTTACACA                         GTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA
genomic: TCAATGAATTGCTTGAGAATATTTACACAgtatgtgtta ... tgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcaactaaggtttcctttccacaatctcaccatgttatgaatttgtctggaagGTGTTGGATTTCTTCAATAGTCGAATGGACATGCAGCAGTTAGATGGAGAATGGTCTGTAGATAAGGTTCTTGAGGTTATTAACAAAAACTGCCGTTCAT
                         atctcac  putative branch site (score: 3)
                                           tttgtct  putative PPT
                                    ttatgaattt  TA-rich tract