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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctggaaaatctgctattttgctactgtatctttttgtaaagaaatgatttgtactttgaaattgatgttcaaacttcactacagGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAAGTTCTGGTCAAGGGGGAACCAAACATATCGTACATCTGCTCCCGATACT

Basic information

species Zea mays
transcript GRMZM2G024151_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 7
gtatgctggaaaatctgctattttgctactgtatctttttgtaa--agaaatgatttgtactt-tgaaattgatgttcaaacttc--actacagGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAAGTTCTGGTCAAGGGGGAACCAAACATATCGTACATCTGCTCCCGATACT
    |   || |||     | |   | ||| | |  | || |||  ||  |   | ||  ||| |       |||| | || ||     |  |||   | ||  |||      |  ||       |  ||| | |   | |  |  |  |  |   || |  ||| || | |   |||| ||  |  |      
----gtaagacaattaagaaatccacaact-tgttatattataagcagttacagtctggtcttatcctccctatgtactaatttgtagGTCAAGGGAGAACCGAACATATCGTACATTTGCTCCCGATACTATAGGGCTCCGGAGCTCATATTT--GGTGCCACCGAATACAC--TACAGCTATTGACATCT--

upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g14860.3 (Oryza sativa), 3'ss of exon 5
gtatgctggaaaatctgctattttgctactgtatctttttgtaaagaaatgatttgtactttgaaattgatgttcaaacttcactacagGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAAGTTCTGGTCAAGGGGGAACCAAACATATCGTACATCTGCTCCCGATACT
||||||| |||  | || ||       |    |  |           | |  | |  |||||  ||||||||||  ||||||    ||||| |||||||| ||||| || || || |||||||||||||| |||||||||||||||                                           
gtatgcttgaatgt-tgttacccattcatctcaaataccaccctcttatttctgta-actttataattgatgtttgaacttctaatcagGTAAACCCACATACCCATCAACTCAAGCTATGTGACTTTGGGAGTGCAAAAGTTCTG-------------------------------------------
















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|211165156|gb|FL324133.1|FL324133
EST:     ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTG                         GTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
genomic: ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
EST: gi|61117965|gb|DN558926.1|DN558926
EST:     ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTG                         GTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
genomic: ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
EST: gi|32849187|gb|CD988868.1|CD988868
EST:     ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTG                         GTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
genomic: ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
EST: gi|61117964|gb|DN558925.1|DN558925
EST:     ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTG                         GTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
genomic: ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
EST: gi|32849241|gb|CD988922.1|CD988922
EST:     ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACANAACCTTCTG                         GTGAACCCACACACCCACCAGCTTAAACTA
genomic: ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAACTA
EST: gi|116824535|gb|EC868155.1|EC868155
EST:     ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTG                         GTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
genomic: ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
EST: gi|61117966|gb|DN558927.1|DN558927
EST:     ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTG                         GTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
genomic: ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
EST: gi|5928717|gb|AW055934.1|AW055934
EST:     ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTG                         GTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
genomic: ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
EST: gi|33097248|gb|CF057208.1|CF057208
EST:     ACTATCGGTGTCTGCCACAGAGATATTAAGCCACAAAATCTTCTG                         GTGAACCCACACACCCACCAGCTTAAAATATGTGACTTTGGTAGTGCAAAA
genomic: ACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
EST: gi|60349962|gb|DN216935.1|DN216935
EST:     ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTG                         GTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
genomic: ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
EST: gi|32863940|gb|CF003622.1|CF003622
EST:     ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTG                         GTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA
genomic: ATGGCACTATTGGTGTCTGCCACAGAGATATTAAGCCACAAAACCTTCTGgtatgctgga ... ttcactacagGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttgtaaagaaatgatttgtactttgaaattgatgttcaaacttcactacagGTGAACCCACACACCCACCAGCTTAAACTATGTGACTTTGGCAGTGCAAAAGTTCTGGTCAAGGGGGAACCAAACATATCGTACATCTGCTCCCGATACT
                              aattgat  putative branch site (score: 4)
                                            cttcact  putative PPT
       taaagaaatgattt  TA-rich tract