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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatttgagatggttgagctttatttcttcatttccttagattagattctctaacagtgtcaagtcttacatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG

Basic information

species Zea mays
transcript GRMZM2G015344_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015344_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g44370.1 (Oryza sativa), 3'ss of exon 2
gtaagtatttgagatggttgagctttatttctt-catttccttagattagattct--ctaacagtgtcaagtcttacatgtg-cagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG
|| || |||||||||||||||   |  ||| ||   |||| |    || |  |||   |||||| | || || ||  |  || ||||||||||||||||||   ||||| |||||||||||||||||||||   ||||| || |||
gtgag-atttgagatggttgaatatcctttgttatgtttcttgctcttggcctcttgttaacagcggcatgtattgaaaatgacagTGTGAGAGAGCAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCGCAGAGCCTCTCAAG
















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|89759746|gb|DY688465.1|DY688465
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|211060404|gb|FL062192.1|FL062192
EST:     TATTCGGCAACGTCGACACAAAGGGTGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGMTGCCCTGAAGTTCCAGTAGCAGAGGGCA
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCA
EST: gi|211057441|gb|FL062189.1|FL062189
EST:     TATTCGGCAACGTCGACACAAAGGGTGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|89251363|gb|DY623149.1|DY623149
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|211057429|gb|FL062177.1|FL062177
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|71318567|gb|DR796043.1|DR796043
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|211057439|gb|FL062187.1|FL062187
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGC
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGC
EST: gi|71449461|gb|DR830511.1|DR830511
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|51871130|gb|CV126014.1|CV126014
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCCCTATTGCTG                         TGTGAGAGAGCAGGACACCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|211054467|gb|FL062173.1|FL062173
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|211054469|gb|FL062175.1|FL062175
EST:     TATTCGGCAACGTCGATACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|211057432|gb|FL062180.1|FL062180
EST:     TATTCGGCAACGTCGACACAAAGGGTGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGC
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGC
EST: gi|76935894|gb|DV174515.1|DV174515
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|211057436|gb|FL062184.1|FL062184
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCC-TGAAGTTCCAGTAGC
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGC
EST: gi|211060405|gb|FL062193.1|FL062193
EST:     TATTCGGCAACGTCGACACAAAGGGTGCAACACGTAACGCGTTATTGCTG                         TGTGAGAGAGCAGGAT
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGAT
EST: gi|32803180|gb|CD955416.1|CD955416
EST:     TATTCGGCAACGTCGACACAAAGGGTGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|71438819|gb|DR819869.1|DR819869
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|78105410|gb|DV523828.1|DV523828
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|94473161|gb|EB702119.1|EB702119
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|211057442|gb|FL062190.1|FL062190
EST:     BATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTT
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTT
EST: gi|149077634|gb|EE166336.2|EE166336
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|76290576|gb|DV030144.1|DV030144
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|211054466|gb|FL062172.1|FL062172
EST:     TATTCGGCAACGTCGACACAAAGGGTGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|211057428|gb|FL062176.1|FL062176
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|211054465|gb|FL062171.1|FL062171
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGA
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGA
EST: gi|211057438|gb|FL062186.1|FL062186
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|211057433|gb|FL062181.1|FL062181
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTC-AGTAGCAGAGGGCAGCCA
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCA
EST: gi|71439185|gb|DR820235.1|DR820235
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|211057437|gb|FL062185.1|FL062185
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGRGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAG
EST: gi|211054468|gb|FL062174.1|FL062174
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
EST: gi|211057431|gb|FL062179.1|FL062179
EST:     TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTG                         TGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG
genomic: TATTCGGCAACGTCGACACAAAGGGCGCAACACGTAACGCGCTATTGCTGgtaagtattt ... acatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttcatttccttagattagattctctaacagtgtcaagtcttacatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG
             ttagatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatttgagatggttgagctttatttcttcatttccttagattagattctctaacagtgtcaagtcttacatgtgcagTGTGAGAGAGCAGGATGCCCTGAAGTTCCAGTAGCAGAGGGCAGCCATGAGCCCCTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG