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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGAATTTAATAACATTCATGTTGTTCTTGCGGGGCTAACAAATACATATTCGCAGTATATTACAACTTTTGAAGAATATGAGATCCAAAGATACGAGgtatgtatatgcgcagctcatttgatgttcagtctgagaacataatatagaatggtacaactatagctagcttgatgctcggtggcccttccgcaattaa...

Basic information

species Zea mays
transcript GRMZM2G180732_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180732_T03 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g43520.2 (Oryza sativa), 5'ss of exon 9
TGGTGAATTTAATAA---CATTCATGTTGTTCTTGCGGGGCTAACAAATACATATTCGCAGTATATTACAACTTTTGAAGAATATGAGATCCAAAGATACGAGgtatgtatatgcgcagctcatttgatgttcagtctgagaacataatatagaatggtacaac-tatagctagcttgatgctcggtggcccttccgcaattaa--
   ||||||| ||||    ||||||||||||||||||||||||||||| |  || || ||||| ||||||||||||||||||||  ||||||||||||| ||||| ||||||  |   || ||| || | |  |   ||| ||||   ||| ||||    |||  || |   | ||    |  |  |     |   || ||  |  
---TGAATTTGATAAAAATATTCATGTTGTTCTTGCGGGGCTAACAAACAGCTACTCTCAGTACATTACAACTTTTGAAGAATACCAGATCCAAAGATATGAGgtgtgtataaacttggc-catctggtctatacattgacaaca--gtattgaatcaggcaaaatagactcatctcatagaccaattcatttatagctatctatg
















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|211014109|gb|FL390335.1|FL390335
EST:     ATTCGCAGTATATTACAACTTTTGAAGAATATGAGATCCAAAGATACGAG                         GGAGCGTCGACGTTGTATGGCCCCCACACATTGAGCGCCTACATTCAGGAG
genomic: ATTCGCAGTATATTACAACTTTTGAAGAATATGAGATCCAAAGATACGAGgtatgtatat ... tttttgccagGGAGCATCGACGTTGTATGGCCCCCACACGTTGAGCGCCTACATTCAGGAG
EST: gi|67039587|gb|CO465842.1|CO465842
EST:     TTCGCAGTATATTACAACTTNTTGAAGAATATGAGATCCNAAGATACGAG                         GGAGCATCGACGTTGTATGGCCCCCACACGNTGAGCGCCTACATTCAGGGA
genomic: TTCGCAGTATATTACAACTT-TTGAAGAATATGAGATCCAAAGATACGAGgtatgtatat ... tttttgccagGGAGCATCGACGTTGTATGGCCCCCACACGTTGAGCGCCTACATTCAGG-A
EST: gi|31353115|gb|CD437472.1|CD437472
EST:     ATTCGCAGTATATTACAACTTTTGAAGAATATGAGATCCAAAGATACGAG                         GGAGCGTCGACGTTGTATGGCCCCCACACATTGAGCGCCTACATTCAGGAG
genomic: ATTCGCAGTATATTACAACTTTTGAAGAATATGAGATCCAAAGATACGAGgtatgtatat ... tttttgccagGGAGCATCGACGTTGTATGGCCCCCACACGTTGAGCGCCTACATTCAGGAG
EST: gi|60399436|gb|DN232248.1|DN232248
EST:     ATATGAGATCCAAAGATACGAG                         GGAGCATCGACGTTGTATGGCCCCCACACGTTGAGCGCCTACATTCAGGAG
genomic: ATATGAGATCCAAAGATACGAGgtatgtatat ... tttttgccagGGAGCATCGACGTTGTATGGCCCCCACACGTTGAGCGCCTACATTCAGGAG
EST: gi|60344985|gb|DN211958.1|DN211958
EST:     ATATGAGATCCAAAGATACGAG                         GGAGCATGGACGTTGTATGGCCCCCACACGTTGAGCGCCTACATTCAGGAG
genomic: ATATGAGATCCAAAGATACGAGgtatgtatat ... tttttgccagGGAGCATCGACGTTGTATGGCCCCCACACGTTGAGCGCCTACATTCAGGAG
EST: gi|40334246|gb|CK368316.1|CK368316
EST:     ATTCGCAGTATATTACAACTTTTGAAGAATATGAGATCCAAAGATACGAG                         GGAGCGTCGACGTTGTATGGCCCCCACACATTGAGCGCCTACATTCAGGAG
genomic: ATTCGCAGTATATTACAACTTTTGAAGAATATGAGATCCAAAGATACGAGgtatgtatat ... tttttgccagGGAGCATCGACGTTGTATGGCCCCCACACGTTGAGCGCCTACATTCAGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGAATTTAATAACATTCATGTTGTTCTTGCGGGGCTAACAAATACATATTCGCAGTATATTACAACTTTTGAAGAATATGAGATCCAAAGATACGAGgtatgtatatgcgcagctcatttgatgttcagtctgagaacataatatagaatggtacaactatagctagcttgatgctcggtggcccttccgcaattaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC