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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcttttctcatctttcattatctattcttctctatggtgttttgtctctaccaaattttatagggcaattgtgtcatagctcaagactgattacgaatgactgatatctgtttgctaatgttctgcagTTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATTTAATATCTGTTTATCAACAGAAG

Basic information

species Oryza sativa
transcript LOC_Os12g40830.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G398107_T01 (Zea mays), 3'ss of exon 4
gtaatcttttctcatctttcattatctattcttctctatggtgttttgtctctaccaaattttataggg-caat---tgtgtcatagctcaagactgattacgaatgactgatatctgtttgctaat-------gttctgcagTTTGTGACCCGGTTCTAGGTGATGAAGGGAAA-CTATATGTCCCTCAGGATTTAATATCTGTTTATCAACAGAAG------
|||| |||||| ||||||   |||| |||     |       | ||  ||| ||  |||||| || ||| |||     || ||||| ||  ||| ||  || | |||  | ||   |||||||||||        || ||||||||| ||||| || |||||||||||||| ||| ||||| || ||||||||  ||| |||||||||||||||||||      
gtaaccttttcccatcttctgttatttatgtgctt-------gcttcttctttagtaaatttaattgggacaagatacgtctcataactagagattggctaggcatggttcattcttgtttgctaattgcaaacattatgcagTTTGCGACCCAGTCCTAGGTGATGAAGGAAAAACTATACGTTCCTCAGGAGCTAACATCTGTTTATCAACAGAAGGTGATT

upper sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G069758_T02 (Zea mays), 3'ss of exon 6
gtaatcttttctcatctttcattatctattcttctctatggtgttttgtctctaccaaattttataggg-caatt-gtgtcatagctcaagactgattacgaatgactgata--tctgtttgctaat-------gttctgcagTTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATTTAATATCTGTTTATCAACAGAAG
|||||||||||||||||||  |||| | |     |   |  | |||  |    |   ||||| | |||| |||||   |||||||||  ||||||| ||   |||  | ||   |||||||||||||        | |||||||||||||||| ||||||||||||||||| ||||||||||| ||||||||  |||||||||||||||||||||||
gtaatcttttctcatcttttgttatttgtatgcttgcttcttctttaataa--atttaatttaacagggacaatttaggtcatagctagagactgactagacatggttaattcttctgtttgctaattgcaaacatgctgcagTTTGTGACCCAGTTCTAGGTGATGAAGGAAAACTATATGTTCCTCAGGAGCTAATATCTGTTTATCAACAGAAG
















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|568331|gb|D39176.1|D39176
EST:     CTGATCTTGTATATG                         TTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATT
genomic: CTGATCTTGTATATGgtaatctttt ... tgttctgcagTTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATT
EST: gi|58661072|gb|CK049752.1|CK049752
EST:     ACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATG                         TTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATT
genomic: ACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATGgtaatctttt ... tgttctgcagTTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATT
EST: gi|66924011|gb|CX110859.1|CX110859
EST:     ACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATG                         TTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATT
genomic: ACTACAAGTTGTTGACAAATTACGATCAGTCAATCCTGATCTTGTATATGgtaatctttt ... tgttctgcagTTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatagctcaagactgattacgaatgactgatatctgtttgctaatgttctgcagTTTGTGACCCGGTTCTAGGTGATGAAGGGAAACTATATGTCCCTCAGGATTTAATATCTGTTTATCAACAGAAG
                                       tgctaat  putative branch site (score: 2)
                                          taatgtt  TA-rich tract