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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgccccggcccgccttgctgctctgggcgccgcgtttgattcacataccaacacgcgcggccgccccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAGCGCGCGGCGCTGGAGCCCGGGGAGAACGTGTGGGTCGACGTCGACGTGC

Basic information

species Zea mays
transcript GRMZM2G010044_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010044_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 2
--------gtacgccccggcccgccttgctgctctgggcgccgcgtttgattcacataccaacacgcgcgg---ccgccccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAGCGCGCGGCGCTGGAGCCCGGGGAGAACGTGTGGGTCGACGTCGACGTGC
           || ||| | |     ||||| ||| |  |      | | | |  || |  |   |   ||    |    ||  | |||||||||||||| ||||||||||| |||||||| |||||| ||||||||||||||||     ||||||||||||||||||||||||| |||||||||||||
gtacggcttctcgacccaggctaggctgctgttctcgatgtgattctcg-tgcggatgcggatgaggatgggactctttgcggtttcagGTGAAGAGCGCCATGACGATGACAGAGAAGATCCTGGCGAGGGCGTCGGAGCGCGCCAGCTTGGAGCCCGGGGAGAACGTGTGGGTGGACGTCGACGTGC
















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|71772889|gb|DR970812.1|DR970812
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|148955521|gb|EC901145.2|EC901145
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|211185238|gb|FL072192.1|FL072192
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|91051662|gb|EB162080.1|EB162080
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|211187633|gb|FL072202.1|FL072202
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|211190029|gb|FL072209.1|FL072209
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGAC
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGAC
EST: gi|76012112|gb|DT939282.1|DT939282
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|211185232|gb|FL072186.1|FL072186
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGTGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|211185240|gb|FL072194.1|FL072194
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAAATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|31355882|gb|CD440239.1|CD440239
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|211187626|gb|FL072195.1|FL072195
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|211187637|gb|FL072206.1|FL072206
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|211185236|gb|FL072190.1|FL072190
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|31354069|gb|CD438426.1|CD438426
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|211187631|gb|FL072200.1|FL072200
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|211187638|gb|FL072207.1|FL072207
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|76909966|gb|DV163627.1|DV163627
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|211187634|gb|FL072203.1|FL072203
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         -TGGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGTCGTCGGA
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTG-AAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGA
EST: gi|211187628|gb|FL072197.1|FL072197
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|211185235|gb|FL072189.1|FL072189
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|211187639|gb|FL072208.1|FL072208
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
EST: gi|211185239|gb|FL072193.1|FL072193
EST:     GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCG                         GTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG
genomic: GCGTGCGCGCCGTCGCTTCGCCCGCGCGCGCCCTGTCGTCCACCGGCTCGgtacgccccg ... ccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgggcgccgcgtttgattcacataccaacacgcgcggccgccccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAGCGCGCGGCGCTGGAGCCCGGGGAGAACGTGTGGGTCGACGTCGACGTGC
             gtttgat  putative branch site (score: 5)
                                           ccccgtctcc  putative PPT
              tttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgccccggcccgccttgctgctctgggcgccgcgtttgattcacataccaacacgcgcggccgccccgtctccagGTGAAGAGCGCGATGACGATGACGGAGAAGATACTGGCGCGGGCGTCGGAGCGCGCGGCGCTGGAGCCCGGGGAGAACGTGTGGGTCGACGTCGACGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA