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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttacttctctacttgagagatttaatatgccttttttttttgacaatttagcatgaaatgaagtataatgctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATG

Basic information

species Zea mays
transcript GRMZM2G029573_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029573_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g47850.3 (Oryza sativa), 3'ss of exon 4
gtttgttacttctctact---tgagagatttaatatgcc-ttttttttttgacaattt--agcatgaaatgaagtataatgctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATG
||  ||  ||| |||| |     | |    | |||||      |||     | |  ||  |   |  ||  || || ||||||| | |||||||||||||||| |||| |||||| |||| |||  | |||||||| ||||||||||||||
gtccgtatcttttctattagtcaataatcatgatatgatgccatttccacaatagcttgtaagttttaacaaattagaatgctcatgcagATGATGAAGAATCGAACCGATGTTTCCTTGCTGGTCTGATCATAAGGAATCTAAGCATATG
















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|211516234|gb|FL052551.1|FL052551
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG                         ATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAA
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAA
EST: gi|31355937|gb|CD440294.1|CD440294
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG                         ATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
EST: gi|211516229|gb|FL052546.1|FL052546
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTNATCCTG                         ATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCA
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCA
EST: gi|31361816|gb|CD446173.1|CD446173
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG                         ATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
EST: gi|211516233|gb|FL052550.1|FL052550
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG                         ATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
EST: gi|211087677|gb|FL052574.1|FL052574
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG                         ATGATGAAGAATCAAACCAATG
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATG
EST: gi|89248122|gb|DY619908.1|DY619908
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG                         ATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
EST: gi|148969434|gb|EE020234.2|EE020234
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG                         ATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
EST: gi|211518587|gb|FL052555.1|FL052555
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG                         ATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
EST: gi|211516232|gb|FL052549.1|FL052549
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG                         ATGATGAAGAATCAAACCAATGTTTTCT-GGTGGCTTAATCATAAGAAATC
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
EST: gi|211289807|gb|FL254557.1|FL254557
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG                         ATGATGAAGAATCAAACCAATGTTT-CTTGGTGGCTTAATCATAAGAAATC
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
EST: gi|71764310|gb|DR962247.1|DR962247
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG                         ATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
EST: gi|211518589|gb|FL052557.1|FL052557
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG                         ATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
EST: gi|211087673|gb|FL052570.1|FL052570
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG                         ATGATGAAGAATCAAACCAATGTTTTC
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATGTTTTC
EST: gi|211287670|gb|FL254548.1|FL254548
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG                         ATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATC
EST: gi|211518596|gb|FL052564.1|FL052564
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTTATCCTG                         ATGATGAAGAATCAAA
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAA
EST: gi|211287675|gb|FL254553.1|FL254553
EST:     GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTG                         ATGATGAAGAATCAAACCAATGTTTTCTTGGTGGGCTTAATCATAAG
genomic: GTTTGTCCTAATGACCAATCCTCATATTGGGAACACTGGCGTTAATCCTGgtttgttact ... gctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGG-CTTAATCATAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgccttttttttttgacaatttagcatgaaatgaagtataatgctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATG
             ttttgac  putative branch site (score: 3)
                                            tgctctt  putative PPT
       ttttttttttgacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttacttctctacttgagagatttaatatgccttttttttttgacaatttagcatgaaatgaagtataatgctcttacagATGATGAAGAATCAAACCAATGTTTTCTTGGTGGCTTAATCATAAGAAATCTAAGCATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA