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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttattgttttattctttcttgctttaatactaatatccactaatactaaaagaaagatttcatcttgccatcacactttttctcgaatatacatg...

Basic information

species Zea mays
transcript GRMZM5G876003_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G876003_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g38060.1 (Oryza sativa), 5'ss of exon 3
TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttattgttttattctttcttgctttaatactaatatccactaatactaaaagaaagatttcatcttgccatcacactttttctcgaatatacatg--
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TGGACAAGATGCATTTGACTACTTCACAAATGAGCCTGATCTTTTTGATGTGgtatgctatgcacttttcatccattttggtaatcttattgtttgctag-atgaattttatctttgaagagtatgggca-acaaattttgaactctgggtggt
















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|76923220|gb|DV169382.1|DV169382
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
EST: gi|211194090|gb|FL377673.1|FL377673
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
EST: gi|76281989|gb|DV021557.1|DV021557
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAG
EST: gi|74240435|gb|DT648349.1|DT648349
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
EST: gi|31354696|gb|CD439053.1|CD439053
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
EST: gi|71435218|gb|DR816268.1|DR816268
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
EST: gi|71429033|gb|DR810083.1|DR810083
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
EST: gi|71434799|gb|DR815849.1|DR815849
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATAACAGGATATCAAGAGCAAATGTCACACTGGC
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATA-CAGGATATCAAGAGCAGATGTCACACTGGC
EST: gi|211163247|gb|FL415263.1|FL415263
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATACCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
EST: gi|78074350|gb|DV502784.1|DV502784
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
EST: gi|50329972|gb|CO525098.1|CO525098
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGAT
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGAT
EST: gi|211327567|gb|FL371066.1|FL371066
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCC
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCC
EST: gi|211025381|gb|FL421226.1|FL421226
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAG
EST: gi|76922748|gb|DV169154.1|DV169154
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
EST: gi|78108382|gb|DV526800.1|DV526800
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAAATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
EST: gi|74245743|gb|DT653657.1|DT653657
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
EST: gi|148948106|gb|EC893615.2|EC893615
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
EST: gi|149071083|gb|EE159484.2|EE159484
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
EST: gi|91055947|gb|EB166365.1|EB166365
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
EST: gi|149100899|gb|EE186995.2|EE186995
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
EST: gi|78080458|gb|DV508870.1|DV508870
EST:     GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTG                         TATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG
genomic: GAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttatt ... tctcttttagTATCATACAGGATATCAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAGAGGATGCATTTGACTACTTCAAAAACGACCCTAATCTTTTTGATGTGgtacgttattgttttattctttcttgctttaatactaatatccactaatactaaaagaaagatttcatcttgccatcacactttttctcgaatatacatg

- GAGAGG
-  AGAGGA
- - GAGGAT
- -  AGGATG