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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatgaatcaaagactttatgtttactggttcatcctttcttttgttgatactttcctttccttattctactgatcattgcccttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG

Basic information

species Zea mays
transcript GRMZM2G174696_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174696_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g20750.1 (Oryza sativa), 3'ss of exon 4
gtagatgaatcaaagactttatgtttactggttcatcctttcttttgttgatactttcctttccttattctactgatcattgcccttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
      | | |  |   |  |||||   ||||| ||| | | | | | |||    |   |||| |||||   ||  | |   | | || |||||||||| || ||| | |||||||| ||||| ||||||||||| |||||||||
------gtacctgaatttgaatgttg--tggttaatcttatgtgt-gatgactgatatttttctttatttggcttttgaaatctcattccccagCTTACTCATGAGCCGCATTACTCCCAAGGAATGTTTAACTTTGACTACAAG
















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|31353843|gb|CD438200.1|CD438200
EST:     GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG                         CTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
genomic: GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAGgtagatgaat ... cttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
EST: gi|51593036|gb|CV072182.1|CV072182
EST:     GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG                         CTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
genomic: GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAGgtagatgaat ... cttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
EST: gi|148944949|gb|EC890114.2|EC890114
EST:     GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG                         CTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
genomic: GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAGgtagatgaat ... cttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
EST: gi|71428447|gb|DR809497.1|DR809497
EST:     GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG                         CTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
genomic: GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAGgtagatgaat ... cttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
EST: gi|76294141|gb|DV033709.1|DV033709
EST:     GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG                         CTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
genomic: GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAGgtagatgaat ... cttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
EST: gi|148937183|gb|EC881364.2|EC881364
EST:     GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG                         CTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACGAG
genomic: GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAGgtagatgaat ... cttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
EST: gi|5268993|gb|AI770957.1|AI770957
EST:     GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG                         CTTACCCAAGAAGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
genomic: GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAGgtagatgaat ... cttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
EST: gi|6095402|gb|AW120069.1|AW120069
EST:     GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG                         CTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
genomic: GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAGgtagatgaat ... cttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
EST: gi|6095403|gb|AW120070.1|AW120070
EST:     GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG                         CTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
genomic: GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAGgtagatgaat ... cttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
EST: gi|149090165|gb|EE179465.2|EE179465
EST:     GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG                         CTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
genomic: GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAGgtagatgaat ... cttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
EST: gi|89762284|gb|DY689955.1|DY689955
EST:     GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG                         CTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
genomic: GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAGgtagatgaat ... cttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
EST: gi|6095404|gb|AW120071.1|AW120071
EST:     GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAG                         CTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
genomic: GTGTGAAATGTGATTTGACAGACAATCTGACGTTGAAAGTAAATGCACAGgtagatgaat ... cttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttttgttgatactttcctttccttattctactgatcattgcccttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG
                               tactgat  putative branch site (score: 2)
                                     tcattgcccttttccc  CT-rich tract
                         ttattcta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagatgaatcaaagactttatgtttactggttcatcctttcttttgttgatactttcctttccttattctactgatcattgcccttttcccagCTTACCCAAGAGGCACATTACTCACAAGGGATGTTTAACTTCGACTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG