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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctattcttgatttgattagttcaattgctggcatttttttaaacagatagtcattacatgctgagaaacatttaacttttgcatatgcttgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAATCATCAGCAGATCCAGGCTATTCTTATTTTGGTGCCCCGGACTTTGATCA

Basic information

species Zea mays
transcript GRMZM2G128080_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128080_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g16100.1 (Oryza sativa), 3'ss of exon 6
-tctatt--cttgatttgattagttcaattgctggcatttttttaaacagatagtcattacatgctgagaaacatttaacttttgcatatgcttgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAATCATCAGCAGATCCAGGCTATTCTTATTTTGGTGCCCCGGACTTTGATCA
 |  |||       | | |    ||  |    ||   || | |   | |     ||  || ||| |   | || ||| ||    |  | |   | | || |||||||||||||||||||||||||||| ||||||||||| ||| |||| |  ||||| || |||||||  || |||| |||||||||| | |||||||| ||
gttgattagtacagtattacctttttgacatatgcagttgtctgggatactatatcgctagatgtttgtagacgtttgaca---gtgtttatgtattttgcagCTTGCTTCAGTGTTCATGTGAGAGGATCAGAGTACATCCCTTTGCTTGGCTCATCTGCTGATCCAGATTACTCTTTTTTTGGTGCCTCAGACTTTGACCA

upper sequence: GRMZM2G128080_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G01340.1 (Glycine max), 3'ss of exon 6
tctattcttgatttgatta-gttcaattgctggcatttttttaaacagatagtcattacatgctgagaaacatttaact--tttgcatatgcttgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAATCATCAGCAGATCCAGGCTATTCTTATTTTGGTGCCCCGGACTTTGATCA---
 |  |||        || | ||   |  |  |   |||| || || | ||  |   |||| | |  |   | |  ||||  ||  |||||| |  |  |  |||||||||  |||||||||||||||| |||||||| ||||| || || | |||  || | |||||| | | ||  |   | || |  || ||  |||| |    
ccccttcccacccaaatgaagtgttagcgaagtatttttctttaagatattctatgtacaagttttg---cttgaaactcgttaacatatgttctttatgtagCTTGCTTTGGTGTTCATGTGAGAGGGTCAGAGTATATTCCACTTCTTGGATC--CAAC-GATCCAAGTTCTTTCTTAGTGGGAGTTCCAGATATTGAACTATG
















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|71328612|gb|DR800970.1|DR800970
EST:     GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATG                         CTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
genomic: GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATGgtattatttc ... tgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
EST: gi|211303843|gb|FL436411.1|FL436411
EST:     GAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATG                         CTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
genomic: GAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATGgtattatttc ... tgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
EST: gi|101382451|gb|EB813281.1|EB813281
EST:     GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATG                         CTTGCTTCAGTGTTCATGTGAGAAGGT-CAGAGTACATTCCTCTGCT
genomic: GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATGgtattatttc ... tgtgtttcagCTTGCTTCAGTGTTCATGTGAGA-GGTTCAGAGTACATTCCTCTGCT
EST: gi|71425688|gb|DR806834.1|DR806834
EST:     GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATG                         CTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
genomic: GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATGgtattatttc ... tgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
EST: gi|71425689|gb|DR806835.1|DR806835
EST:     GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATG                         CTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
genomic: GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATGgtattatttc ... tgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
EST: gi|211109868|gb|FL467765.1|FL467765
EST:     GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATG                         CTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCAAGAAT
genomic: GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATGgtattatttc ... tgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
EST: gi|60356030|gb|DN223003.1|DN223003
EST:     GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATG                         CTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
genomic: GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATGgtattatttc ... tgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
EST: gi|60353914|gb|DN220887.1|DN220887
EST:     GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATG                         CTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCTTCTGCTAGAAT
genomic: GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATGgtattatttc ... tgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
EST: gi|78124658|gb|DV543042.1|DV543042
EST:     GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATG                         CTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTTTGCTAGAAT
genomic: GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATGgtattatttc ... tgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
EST: gi|4804244|gb|AI666110.1|AI666110
EST:     GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATG                         CTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
genomic: GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATGgtattatttc ... tgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
EST: gi|71328613|gb|DR800971.1|DR800971
EST:     GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATG                         CTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
genomic: GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATGgtattatttc ... tgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
EST: gi|60343645|gb|DN210618.1|DN210618
EST:     GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATG                         CTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT
genomic: GAAGAAGAAAATGGAGGTCATGCTGCAAAGTGTAGTAAAAATTGAGAATGgtattatttc ... tgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatagtcattacatgctgagaaacatttaacttttgcatatgcttgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAATCATCAGCAGATCCAGGCTATTCTTATTTTGGTGCCCCGGACTTTGATCA
                         atttaac  putative branch site (score: 3)
                     aaacatttaactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctattcttgatttgattagttcaattgctggcatttttttaaacagatagtcattacatgctgagaaacatttaacttttgcatatgcttgtgtttcagCTTGCTTCAGTGTTCATGTGAGAGGTTCAGAGTACATTCCTCTGCTAGAATCATCAGCAGATCCAGGCTATTCTTATTTTGGTGCCCCGGACTTTGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT