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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgttcaactgcttttacaatctcttaaatcactattgggcgctacatactatgttgctcagttatacatttctttcatttactagGGAAATGAGGCTCCAGCTCCATTCATGACATTTCAGTCCACAGGTTTCCCTCCAGAGATTCTAAGGGAG

Basic information

species Oryza sativa
transcript LOC_Os01g07740.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07740.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G481227_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------------gtatgtgttcaactgcttt-tacaatctcttaaatcactattgggcgcta-catacta---tgttgctcagttatacatttctttcatttac-----tagGGAAATGAGGCTCCAGCTCCATTCATGACATTTCAGTCCACAGGTTTCCCTCCAGAGATTCTAAGGGAG
                                                           |||||| ||||||  |   |    | | |||  | | | ||   | | | ||  ||    | ||| | ||||||  | || |||||||||      ||||| |||||||| || || ||||||||||||||||| |||||||| |||||   ||| ||||||||||||
gtggacaagaaacaaaattttggtcgtatgtgatttacaaatccatccattttactttttatgtggtcaactaatccatttctttttttatttaaatgttaccctcaatcactcttgttttttgtttagttat-tacttttttcatttatattaatagGGCAATGAGGCACCTGCACCATTCATGACATTTCAATCCACAGGCTTCCCATTAGACATTCTAAGGGAG

upper sequence: LOC_Os01g07740.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G462134_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------------gtatgtgttcaactg-----cttttacaatctcttaaat--cactattgggcgctacatactatgttgctcagttatacatttct--ttcat-ttactagGGAAATGAGGCTCCAGCTCCATTCATGACATTTCAGTCCACAGGTTTCCCTCCAGAGATTCTAAGGGAG
                                                           |||||| ||||||       || |    |   ||||||   ||  |    | || | |  ||| ||  | ||||||   ||| |  || || ||| ||||| |||||||| || || ||||||||||||||||| |||||||| || ||   ||| ||||||||||||
gtggacaagaaacaaaattttggtcgtatgtgatttacaaatccatccattttactttttatgtggtcaactaatccatttctttttttatttaaatgttaccctcaatcact-cttgttattttatttagttattactttttcatttatattaatagGGCAATGAGGCACCTGCACCATTCATGACATTTCAATCCACAGGCTTACCATTAGACATTCTAAGGGAG

upper sequence: LOC_Os01g07740.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G066440_T01 (Zea mays), 3'ss of exon 4
-------------gtatgtgttcaactgcttttacaatct---cttaaatcactattgggcgctacatact---atgttgctcagttatacatttc---tttcatttactagGGAAATGAGGCTCCAGCTCCATTCATGACATTTCAGTCCACAGGTTTCCCTCCAGAGATTCTAAGGGAG
               ||   ||||  |  ||||  ||| |     | |  | | |     ||     || |     ||| || |  | |   ||||   |||  | ||  |||| || ||| | || || |||||||||||||||||||||||| | |||||  |||| ||||||||||||
gtatgtgataaactaatccattcattttattttttaatttaaatgttaccctcaaccactcgtcttttatttaagcgttacttaaatttttttttccatttttttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG

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|2310452|gb|C26607.1|C26607
EST:     ATCGTGCTAAGCA-NAGCATCACTATTGTC                         GGAAATNAGGCTCCAGCTCCATTCATGACATTTCAGTCCACAGGTTTCCCT
genomic: ATCGTGCTAAGCACGAG-ATCACTATTGTCgtatgtgttc ... catttactagGGAAATGAGGCTCCAGCTCCATTCATGACATTTCAGTCCACAGGTTTCCCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actattgggcgctacatactatgttgctcagttatacatttctttcatttactagGGAAATGAGGCTCCAGCTCCATTCATGACATTTCAGTCCACAGGTTTCCCTCCAGAGATTCTAAGGGAG
                                      tttctttcatttact  CT-rich tract
                               ttatacatttcttt  TA-rich tract