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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggttattttctttgttttttaatgacaaaaatagttaacctttcatatctatacttgtgcttgaatacatacgtccctgctgacgcgttctactgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATT

Basic information

species Zea mays
transcript GRMZM2G164175_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164175_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g02110.1 (Oryza sativa), 3'ss of exon 6
gtggttat--tttctttgttttttaatgacaaaaatagttaacctttcatatctatac-ttgtgcttgaatacatacgtccctgctgacgcgttctact-gcactcagTGATAG-CAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATT
||| |||| ||| | |||| || || | ||| || | |||||| | || |||| | ||| | | | | ||||| | || | ||| || | ||||||||||||||||||||||||||||||||| | | ||||| || ||||| ||| |||||||||||||||||||| | |||||||||||
gtgattatgccttcacttttttctagtgcagtagata--tagcatttcattttactatgttgtacctgatt-tagccaattatcctgacttagcgtgcttgttaccagCGAAAAACAAAGGGACCTTGGATGAGTCAGATCGTTTCCTCATGAACCCATCAGATTTTGTGGGCAAGGTTTTTGGAAATTTATCTTCTTTCAGTCACAT-

upper sequence: GRMZM2G164175_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g39810.4 (Oryza sativa), 3'ss of exon 5
gtggttattttctttgttttttaatgacaaaaatagttaacctttcatatctatac-ttgtgcttgaatacatacgtccctgctgacgcgttctac-tgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATT
||| ||||| | || || ||| | | | | | || | |||| | | | |||| | | | | | | ||||| | | | || |||||| | |||||||||||||||||||||||| |||||||| | | ||| | || ||||| |||||||||||||||||||||||| | |||||||| |||
gtgattattct-ttcattgtttctagtccagtagatatagcatttctttttaccatgttgtaccc-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|40336287|gb|CK370357.1|CK370357
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|71427411|gb|DR808461.1|DR808461
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|71314140|gb|DR793687.1|DR793687
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|71764471|gb|DR962408.1|DR962408
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|6654204|gb|AW267609.1|AW267609
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|88748600|gb|DY532741.1|DY532741
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|71321848|gb|DR797614.1|DR797614
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|76932561|gb|DV173073.1|DV173073
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|4826073|gb|AI667701.1|AI667701
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|211236953|gb|FK974486.1|FK974486
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTKGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|211236952|gb|FK974485.1|FK974485
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|211131602|gb|FL458961.1|FL458961
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTYCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|148948729|gb|EC898651.2|EC898651
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATT
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
EST: gi|37392942|gb|CF633725.1|CF633725
EST:     TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAG                         TGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC
genomic: TCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttattt ... ctgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctatacttgtgcttgaatacatacgtccctgctgacgcgttctactgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATT
                              tgctgac  putative branch site (score: 2)
 ttctact  putative PPT
 aatacata  TA-rich tract