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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcatttgtttttaagggaaaattctttagtgtttcttattgtctgcactgttatatacatttactgttagcatggtcctttgagctactttatcatttttttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG

Basic information

species Zea mays
transcript GRMZM2G136389_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136389_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g07990.1 (Oryza sativa), 3'ss of exon 3
gtaaggcatttgtttttaagggaaaattctttagtgtttcttattgtctgcactgtt----atatacatttactgttagcatggtcctttgagctactttatcatt-tttttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
|| ||   ||  |||  |||  ||  || |  ||  |    | |||| || |||| |    | |||   | | || || | |  |  ||     |  |||| |||  ||||| ||||||||||||||||||||| ||||| |||||||||||  ||
gttagtgtttgatttgcaagcaaattttatgcagcctcctctgttgtttgtactgcttttaacatatgatcagtgctatcctcatggttgacatttatttaccatcatttttactgcagCTATGTTGAAAGCTTCAAAAGGAAGTTTGCATCGCAG
















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|89247752|gb|DY619538.1|DY619538
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|78114509|gb|DV532898.1|DV532898
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|71319331|gb|DR796417.1|DR796417
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|76291396|gb|DV030964.1|DV030964
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|15100324|gb|BI396115.1|BI396115
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|89758710|gb|DY687791.1|DY687791
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|50323554|gb|CO518680.1|CO518680
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|71431214|gb|DR812264.1|DR812264
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|18963822|gb|BM660649.1|BM660649
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|71431215|gb|DR812265.1|DR812265
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|101382964|gb|EB813535.1|EB813535
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|91878484|gb|EB408441.1|EB408441
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGC
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGC
EST: gi|91876453|gb|EB406410.1|EB406410
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|94472235|gb|EB701193.1|EB701193
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|87153075|gb|DY397864.1|DY397864
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|71429124|gb|DR810174.1|DR810174
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|71307824|gb|DR790133.1|DR790133
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGGTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|78114508|gb|DV532897.1|DV532897
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
EST: gi|149009815|gb|EE041700.2|EE041700
EST:     GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCG                         CTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
genomic: GCTGCATGGTTGAGAGCAGAAGATCAGTATGAAAATGAGTCAGGCAATCGgtaaggcatt ... tttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacatttactgttagcatggtcctttgagctactttatcatttttttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG
                              ctactttatcattttt  CT-rich tract
                               tactttatcatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggcatttgtttttaagggaaaattctttagtgtttcttattgtctgcactgttatatacatttactgttagcatggtcctttgagctactttatcatttttttcctgcagCTATGTTGAAAGCTTTAAAAGAAAGTTTGCATCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA