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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgattcaaaatgctttgatgcttccgtattccatttttcttatattgaccctcttgtattttatgatatggttgatatataggtaagaatacattttcttcagtgtaacacttaaccaaactacatcgtgcagGTTGTTGCAGTGAAGCAACTTGATCGCAATGGCCTTCAAGGAAACAGGGAGTTTCTGGTTGAGGTTCTAATGCTTAGTCTGTTGCACCATGACAATCTAG

Basic information

species Zea mays
transcript GRMZM2G140590_T06
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140590_T06 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g30870.1 (Oryza sativa), 3'ss of exon 2
gtttgtgattcaaaatgctttgatgcttccgtattccatttttcttatattgaccctcttgtattttatgatatggttgatatataggtaagaatacattttcttcagtgtaacacttaaccaaactac--atcgtgcagGTTGTTGCAGTGAAGCAACTTGATCGCAATGGCCTTCAAGGAAACAGGGAGTTTCTGGTTGAGGTTCTAATGCTTAGTCTGTTGCACCATGACAATCTAG
                                     ||  ||  |  |||   | | |       ||||  ||   ||    ||  |     | |  ||| ||| |  ||     |  |  |   |||  |   |||||| |||||||||||||||||||||||||||||| ||||||||||| || |||||||||||||| || || ||||| ||||| ||||||||||| || || |
-------------------------------------atggttactgcatt--tcttttaaccccctatgtgatctgtggagcattagaggagacatgtttccttaaa-gtcttgatcgatgagcttaccaaatatgcagGCTGTTGCAGTGAAGCAACTTGATCGCAATGGACTTCAAGGAAATAGAGAGTTTCTGGTTGAAGTCCTTATGCTCAGTCTATTGCACCATGATAACCTGG

upper sequence: GRMZM2G140590_T06 (Zea mays), 3'ss of exon 1
lower sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
gtttgtgattcaaaatgctttgatgcttccgtattccatttttcttatattgaccctcttgtattttatgatatggttgatatataggtaagaatacattttcttcagtgtaacacttaaccaa--actacatcgtgcagGTTGTTGCAGTGAAGCAACTTGATCGCAATGGCCTTCAAGGAAACAGGGAGTTTCTGGTTGAGGTTCTAATGCTTAGTCTGTTGCACCATGACAATCTAG
                                     || |||  ||||| ||      || |||     |||  ||| ||   |  ||   |     | ||  |   | |     | ||  ||  | |  ||  ||||||| ||||| ||||| |||||||| || ||||||||||||||||| || || ||  |||| |||||||| |||||||| || || || ||    || || |
------------------------------------aatcttttatatatggaata---tggattgctgaataatgttaatcactgtgtctcatctggtatttattgatttttggttcaatgaattattgtatt-tgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG

upper sequence: GRMZM2G140590_T06 (Zea mays), 3'ss of exon 1
lower sequence: PP1S116_107V6.1 (Physcomitrella patens), 3'ss of exon 2
gtttgtgattcaaaatgctttgatgcttccgtattccatttttcttatattgaccctcttgtattttatgatatggttgat-atataggtaagaatacattttctt-cagtgtaacacttaaccaaactacatcg----------tgcagGTTGTTGCAGTGAAGCAACTTGATCGCAATGGCCTTCAAGGAAACAGGGAGTTTCTGGTTGAGGTTCTAATGCTTAGTCTGTTGCACCATGACAATCTAG
                                                  ||    | ||  |   ||||  |||| |||  ||||  |   |    ||  |   |   | | |  ||    |  |      | |          ||||||| || |||||||||||||| ||||| || || || ||||| ||| | ||||||||||| || ||  | ||||| ||||||||||| |||   ||||| |
--------------------------------------------------tggaatttttacaccgtatggaatgggtgaggatattagagggcgagcaggtgaatgtggcggaggacgaggctgaggggtgttgagtgggtggttgcagGTGGTGGCAGTGAAGCAACTGGATCGGAACGGGCTGCAAGGGAACCGAGAGTTTCTGGTAGAAGTGTTGATGCTGAGTCTGTTGCATCATCCGAATCTCG

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|32830961|gb|CD970639.1|CD970639
EST:     GTGAGGGAGGTTTTGGTCGTGTTTATAAAGGACGTTTGGAGAATGGACAG                         GTTGTTGCAGTGAAGCAACTTGATCGCAATGGCCTTCAAGGAAACAGGGAG
genomic: GTGAGGGAGGTTTTGGTCGTGTTTATAAAGGACGTTTGGAGAATGGACAGgtttgtgatt ... catcgtgcagGTTGTTGCAGTGAAGCAACTTGATCGCAATGGCCTTCAAGGAAACAGGGAG
EST: gi|71321773|gb|DR797574.1|DR797574
EST:     GTGAGGGAGGTTTTGGTCGTGTTTATAAAGGACGTTTGGAGAATGGACAG                         GTTGTTGCAGTGAAGCAACTTGATCGCAATGGCCTTCAAGGAAACAGGGAG
genomic: GTGAGGGAGGTTTTGGTCGTGTTTATAAAGGACGTTTGGAGAATGGACAGgtttgtgatt ... catcgtgcagGTTGTTGCAGTGAAGCAACTTGATCGCAATGGCCTTCAAGGAAACAGGGAG
EST: gi|33100194|gb|CF060154.1|CF060154
EST:     GTGAGGGAGGTTTTGGTCGTGTTTATAAAGGACGTTTGGAGAATGGACAG                         GTTGTTGCAGTGAAGCAACTTGATCGCAATGGCCTTCAAGGAAACAGGGAG
genomic: GTGAGGGAGGTTTTGGTCGTGTTTATAAAGGACGTTTGGAGAATGGACAGgtttgtgatt ... catcgtgcagGTTGTTGCAGTGAAGCAACTTGATCGCAATGGCCTTCAAGGAAACAGGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataggtaagaatacattttcttcagtgtaacacttaaccaaactacatcgtgcagGTTGTTGCAGTGAAGCAACTTGATCGCAATGGCCTTCAAGGAAACAGGGAGTTTCTGGTTGAGGTTCTAATGCTTAGTCTGTTGCACCATGACAATCTAG
                               acttaac  putative branch site (score: 3)
     taagaatacatttt  TA-rich tract