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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggattcaattcttgacactgaattgcatgatttacaaagaactgacaaatatgtacattcttagttaaactcatcatatctcacatattcctcctgctgttctgttctgtccttttagAATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTGACCTTCTATAAGTTGACGCACCCACTGGACAAGTCATGGCATGTTCTTG

Basic information

species Zea mays
transcript GRMZM2G386971_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G386971_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 8
gtgaggattcaattcttgacactgaattgcatgatttacaaagaactgacaaatatgtacattcttagttaaactcatcatatctcacatattcctcctgctgttctgttctgtccttttagAATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTGACCTTCTATAAGTTGACGCACCCACTGGACAAGTCATGGCATGTTCTTG
|||||  | | | | |    | || ||  |||   ||  | ||||   ||    ||| |    | |  || |    | |||        ||||| | ||  | ||||        ||   ||||||||||| |||| ||||||||||||||||| ||||| ||||||||||| |||||||| ||||||||||| || || |||||||| |||||||| ||||
gtgagactactactttcattattggatcacattgatt-tagagaagaaactgtaatgcaa---catgatttagtctaacat--------tattcttgctatttttct-------tctaacagAATGAAGACCGGGTTCTTTGGAAGCTTGGGACGCTTCCACCTGGCCTCTTAACCTTCTACAAGTTGACGCATCCCCTTGACAAGTCGTGGCATGTCCTTG

upper sequence: GRMZM2G386971_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os09g36180.1 (Oryza sativa), 3'ss of exon 9
gtgaggattcaattcttgacactgaattgcat-gatttacaaagaactgacaaatatgtacattcttagttaaactcatcatatctcacatattcctcctgctgttctgttctgtccttttagAATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTGACCTTCTATAAGTTGACGCACCCACTGGACAAGTCATGGCATGTTCTTG
|||||  | | | |      | || ||  ||| |||||| | |   |   ||||    |  | ||| |        |||||        || || ||  |    || | || | | ||   |||| |||||| |||| ||||||||||||||||||||||| |  ||||||||||||||||  ||||||||||| || || |||||||| |||||||| || |
gtgagattactacttccatgattggatctcattgatttagagatgtcatgcaaaacgatttactctaa--------catca--------atgttgctttt----tttttttttcttctaacagAACGAAGACCGGGTTCTTTGGAAGCTTGGGACACTTCCACACGGCCTCTTGACCTTCTTCAAGTTGACGCATCCCCTTGACAAGTCGTGGCATGTCCTCG
















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|67031422|gb|CO460171.1|CO460171
EST:     TGGAAGAAAGAA-GATATTACTGGGATCTACCCACAA-TGGCAAA-TATG                         AATGAAGACAGGNTCCTTTGGAA
genomic: TGGAAGAA-GAAAGATATTACTGGGATCTACC-ACAAATGGCAAAATATGgtgaggattc ... gtccttttagAATGAAGACAGGGTCCTTTGGAA
EST: gi|60356223|gb|DN223196.1|DN223196
EST:     AGTGGAAGAAGAAAGATATTACTGGGATCTACCACAAATGGCAAAATATG                         AATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTG
genomic: AGTGGAAGAAGAAAGATATTACTGGGATCTACCACAAATGGCAAAATATGgtgaggattc ... gtccttttagAATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTG
EST: gi|71428872|gb|DR809922.1|DR809922
EST:     AGAAGAAAGATATTACTGGGATCTACCCCAAATGGCAAAATATG                         AATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTG
genomic: AGAAGAAAGATATTACTGGGATCTACCACAAATGGCAAAATATGgtgaggattc ... gtccttttagAATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTG
EST: gi|32945867|gb|CF050686.1|CF050686
EST:     AGTGGAAGAAGAAAGATATTACTGGGATCTACCACAAATGGCAAAATATG                         AATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTG
genomic: AGTGGAAGAAGAAAGATATTACTGGGATCTACCACAAATGGCAAAATATGgtgaggattc ... gtccttttagAATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTG
EST: gi|71429812|gb|DR810862.1|DR810862
EST:     AGAAGAAAGATATTACTGGGATCTACCACAAATGGCAAAATATG                         AATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTG
genomic: AGAAGAAAGATATTACTGGGATCTACCACAAATGGCAAAATATGgtgaggattc ... gtccttttagAATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTG
EST: gi|71429813|gb|DR810863.1|DR810863
EST:     AGTGGAAGAAGAAAGATATTACTGGGATCTACCACAAATGGCAAAATATG                         AATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTG
genomic: AGTGGAAGAAGAAAGATATTACTGGGATCTACCACAAATGGCAAAATATGgtgaggattc ... gtccttttagAATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTG
EST: gi|32805763|gb|CD957997.1|CD957997
EST:     GATCTACCACAAATGGCAAAATATG                         AATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTG
genomic: GATCTACCACAAATGGCAAAATATGgtgaggattc ... gtccttttagAATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaaactcatcatatctcacatattcctcctgctgttctgttctgtccttttagAATGAAGACAGGGTCCTTTGGAAGCTTGGGACACTTCCGCCTGGCCTCTTGACCTTCTATAAGTTGACGCACCCACTGGACAAGTCATGGCATGTTCTTG
              atctcac  putative branch site (score: 3)
                        ttcctcctgctgttct  putative PPT
         atcatat  TA-rich tract