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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggttattttatttgttttttaatgaaaaaaatagttaacctttcatatctatacttgtgcttgaatacatatgtccctgctgactcgttctactgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGATGTTTTTGGAAATTTATCTGCATTCAGTCACATT

Basic information

species Zea mays
transcript GRMZM2G000937_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000937_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g02110.1 (Oryza sativa), 3'ss of exon 6
gtggttat--tttatttgttttttaatgaaaaaaatagttaacctttcatatctatac-ttgtgcttgaatacatatgtccctgctgactcgttctact-gcactcagTGATAG-CAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGATGTTTTTGGAAATTTATCTGCATTCAGTCACATT
||| ||||   ||   | |||| || || |  | |||  || | |||||| |   ||  |||| | ||| |  |        | ||||||     | || |    ||| || |  ||||||||||||||||||||||||||||||||| |  |  ||||| || ||||| ||| | |||||||||||||||||| | ||||||||||| 
gtgattatgccttcacttttttctagtgcagtagata--tagcatttcattttactatgttgtacctgatt-tagccaattatcctgacttagcgtgcttgttaccagCGAAAAACAAAGGGACCTTGGATGAGTCAGATCGTTTCCTCATGAACCCATCAGATTTTGTGGGCAAGGTTTTTGGAAATTTATCTTCTTTCAGTCACAT-

upper sequence: GRMZM2G000937_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g39810.4 (Oryza sativa), 3'ss of exon 5
gtggttattttatt-tgttttttaatgaaaaaaatagttaacctttcatatctatacttgtgcttgaatacatatgtccctgctgactcgttctac-tgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGATGTTTTTGGAAATTTATCTGCATTCAGTCACATT
||| ||||| | |  |  ||| || |  |  | |||    |  | |  |  | ||  |||| |   |  | |        | ||||||   | | | ||    |||||| | |||||||||||||||||||||||| |||||||| |  |  ||| | || ||||| ||||| |||||||||||||||||| | |||||||| |||
gtgattattctttcattgtttctagtccagtagatatagcatttctttttaccatg-ttgtaccc-atcatagccaattatcctgacttagtttgcatgttaccagTGAAAACAAAGGGACCTTGGATGAGTCAGACCGTTTCCTCATGAACCCAGCAGATTTTGTGGGCGAGGTTTTTGGAAATTTATCTTCGTTCAGTCATATT
















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|110506408|gb|EE017968.1|EE017968
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGGTTTCCTTACAAGTCCA
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTA-Ggtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATC-GTTTCCTTACAAGTCCA
EST: gi|148929350|gb|EC875261.2|EC875261
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|6653847|gb|AW267252.1|AW267252
EST:     TCAACCTTCCATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|211018072|gb|FL437095.1|FL437095
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatacttgtgcttgaatacatatgtccctgctgactcgttctactgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGATGTTTTTGGAAATTTATCTGCATTCAGTCACATT
                              tgctgac  putative branch site (score: 2)
                                        ttctact  putative PPT
                aatacatat  TA-rich tract