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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCTGAGAGATGCAGAAAATGCAAAGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttgtgttgtactcagggtatcattgaatcatcagtaatagctgtgaagaaataaatggatcaactgtcacattaagctttctgtttgggtcttcaatccattgtcatgcaattagggcatttcatttcag

Basic information

species Zea mays
transcript GRMZM2G017086_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017086_T03 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 14
ATGCTGAGAGATGCAGAAAATGCAAAGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttgtgttgtactcagggtatcattgaatcatcagta-atagctgtgaagaaataaatggatcaactgt------------cacattaagctttctg-------tttgggtcttcaatccattgtcatgcaattagggcatttcatttcag
||||||||||||||||||||||| ||||||||||| ||||||||||| || || ||| |||  ||||||||||||||||||||  |   | |       |||  |||| ||||||||  | || |||  ||| ||      ||||    |            ||  |||| |  ||         ||| |  ||| ||   ||  | | | | ||   ||| ||||||||||
ATGCTGAGAGATGCAGAAAATGCTAAGTTTGGATTAAAAGCACAAGGAAAGGCCAGCAGCTCAAAAGAAAATGAGgtaatggtctttaggaat-----atatggttgattcatcagtttagagttgttgagacatgcgcttatcattcttttgttgagcacacatgttaaccactccaaaatgccttttgtacttgaacggatccttacggagtt---gcacttcatttcag
















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|33093217|gb|CF053211.1|CF053211
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|5932702|gb|AW057063.1|AW057063
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|32930058|gb|CF034870.1|CF034870
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|33094822|gb|CF054816.1|CF054816
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|6056638|gb|AW091043.1|AW091043
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|5846961|gb|AW000040.1|AW000040
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|12968043|gb|BG264990.1|BG264990
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|32866634|gb|CF006316.1|CF006316
EST:     AGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|32942933|gb|CF047752.1|CF047752
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|31910881|gb|CD651645.1|CD651645
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|67013124|gb|CO441873.1|CO441873
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|5901176|gb|AW042276.1|AW042276
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|32933054|gb|CF037866.1|CF037866
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|5296339|gb|AI783109.1|AI783109
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|32934559|gb|CF039371.1|CF039371
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|16378498|gb|BI992465.1|BI992465
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|60352250|gb|DN219223.1|DN219223
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|12968042|gb|BG264989.1|BG264989
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGGCAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|50332355|gb|CO527481.1|CO527481
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|32932375|gb|CF037187.1|CF037187
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|32930666|gb|CF035478.1|CF035478
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|74240014|gb|DT647928.1|DT647928
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|33093538|gb|CF053532.1|CF053532
EST:     AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
genomic: AGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG
EST: gi|5919412|gb|AW054509.1|AW054509
EST:     AAAGCTAGCGGCTTTAAAGAAAATGAG                         GGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGCCATTGCCAAAG
genomic: AAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttg ... ttcatttcagGGATCATCCAGTAGCGCTGGGGAATCATCCAGTATGGACATTGACAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCTGAGAGATGCAGAAAATGCAAAGTTTGGATTGAAAGCACAAGGGAAAGCTAGCGGCTTTAAAGAAAATGAGgtaatggttgtgttgtactcagggtatcattgaatcatcagtaatagctgtgaagaaataaatggatcaactgtcacattaagctttctgtttgggtcttcaatccattgtcatgcaattagggcatttcatttcag

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