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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgatatagaacatagaccaagctcctgggtgatttttttcttctttgcaacaattgttcatttcactcattgacgagatctctctctctacttttcagTAAGCAAAGATGGCACCACCATCCATGTGTCTTGCGGCAAAGGGGGTGCTTCCCTTCTCGGCACTTATTTCAAGTGGTGTTACACAAAGGCCAGTGTCAG

Basic information

species Zea mays
transcript GRMZM2G110408_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110408_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g45820.1 (Oryza sativa), 3'ss of exon 1
--gatgatatag--aacatagaccaagctcctgggtgatttttttcttctttgcaacaattgttcatttcactcattgacgagatctctctctc--tactttt--cagTAAGCAAAGATGGCACCACCATCCATGTGTCTTGCGGCAAAGGGGGTGCTTCCCTTCTCGGCACTTATTTCAAGTGGTGTTACACAAAGGCCAGTGTCAG
   ||||  |    | | |||   |||   | |    |    ||||| |  | ||||| ||||           |||||| ||||||| || ||  |||||||  |||| ||| |||||||| ||| |||||||| | ||||| ||||||  |  ||||||||||||| |||||  ||| ||||| ||| |||| |||||||| || |
gatatgaagtgattagcttagttgaagtatcggatgaagcaatttctgccatacaacacttgtatg--------attgacaagatctccctttcattacttttaacagTGAGCGAAGATGGCTCCAACATCCATGAGCCTTGCTGCAAAGACGCCGCTTCCCTTCTCGACACTTCCTTCGAGTGGCGTTGCACAGAGGCCAGTTTCTG
















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|148955092|gb|EC900606.2|EC900606
EST:     AAAATCTGCGCCAGTTCGCCTCGCCTACTTATACACTCCGATCGCCCCCG                         TAAGCAAAGATGGCACCACCATCCATGTGTCTTGCGGCAAAGGGGGTGCTT
genomic: AAAATCTGCGCCAGTTCGCCTCGCCTACTTATACACTCCGATCGCCCCCGgtagttactc ... tacttttcagTAAGCAAAGATGGCACCACCATCCATGTGTCTTGCGGCAAAGGGGGTGCTT
EST: gi|211488280|gb|FL067659.1|FL067659
EST:     AAAATCTGCGCCAGTTCGCCTCGCCTACTTATACACTCCGATCGCCCCCG                         TAAGCAAAGATGGCACCACCATCCATGTGTCTTGCGGCAAAGGGGGTGCTT
genomic: AAAATCTGCGCCAGTTCGCCTCGCCTACTTATACACTCCGATCGCCCCCGgtagttactc ... tacttttcagTAAGCAAAGATGGCACCACCATCCATGTGTCTTGCGGCAAAGGGGGTGCTT
EST: gi|16922886|gb|BM075878.1|BM075878
EST:     AAAATCTGCGCCAGTTCGCCTCGCCTACTTATACACTCCGATCGCCCCCG                         TAAGCAAAGATGGCACCACCATCCATGTGTCTTGCGGCAAAGGGGGTGCTT
genomic: AAAATCTGCGCCAGTTCGCCTCGCCTACTTATACACTCCGATCGCCCCCGgtagttactc ... tacttttcagTAAGCAAAGATGGCACCACCATCCATGTGTCTTGCGGCAAAGGGGGTGCTT
EST: gi|148945970|gb|EC891263.2|EC891263
EST:     AAAATCTGCGCCAGTTCGCCTCGCCTACTTATACACTCCGATCGCCCCCG                         TAAGCAAAGATGGCACCACCATCCATGTGTCTTGCGGCAAAGGGGGTGCTT
genomic: AAAATCTGCGCCAGTTCGCCTCGCCTACTTATACACTCCGATCGCCCCCGgtagttactc ... tacttttcagTAAGCAAAGATGGCACCACCATCCATGTGTCTTGCGGCAAAGGGGGTGCTT
EST: gi|93283958|gb|EB676222.1|EB676222
EST:     AAAATCTGCGCCAGTTCGCCTCGCCTACTTATACACTCCGATCGCCCCCG                         TAAGCAAAGATGGCACCACCATCCATGTGTCTTGCGGCAAAGGGGGTGCTT
genomic: AAAATCTGCGCCAGTTCGCCTCGCCTACTTATACACTCCGATCGCCCCCGgtagttactc ... tacttttcagTAAGCAAAGATGGCACCACCATCCATGTGTCTTGCGGCAAAGGGGGTGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcaacaattgttcatttcactcattgacgagatctctctctctacttttcagTAAGCAAAGATGGCACCACCATCCATGTGTCTTGCGGCAAAGGGGGTGCTTCCCTTCTCGGCACTTATTTCAAGTGGTGTTACACAAAGGCCAGTGTCAG
                        cattgac  putative branch site (score: 3)
                                   tctctctctctacttt  putative PPT
     aacaatt  TA-rich tract