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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgcttatctttttgtaacatttatgttgtgcttatctttttgtaacatttatcagcatatactaaagtataccagtttactaattatctgcctatcagTTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGCGACAAATCAAGGGACAAACTAGATCAGAAG

Basic information

species Zea mays
transcript GRMZM2G125243_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G125243_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g59350.1 (Oryza sativa), 3'ss of exon 4
tatgcttatctttttgtaacatttatgttgtgcttatctttttgtaacattta----tcagcatatactaaagtataccagtttactaattatctg--cctatcagTTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGCGACAAATCAAGGGACAAACTAGATCAGAAG
       ||  |||||||  ||||    | |  ||||  |||| |    || |    | |   |||||| ||  ||| |  |||| |   ||| |   | || ||||||||||||||||   | ||||  ||||| || ||||||||||| ||||  |||| ||||||||||||||| |||
------aattattttgtattattttcactttatttatgcttttttggggttgaatgctaaatttatactcaatcatatcgatttattggctatatatacttaacagTTTGAACAAGGACAGTTAGCTGCTCCCACTGCTTCTGATTCTAGTGACAGGTCAAAGGACAAACTAGATCATAAG
















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|211164177|gb|FL132752.1|FL132752
EST:     CCAGACACTGATGAGAGGAACCAGATG                         TTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGTGACAAA
genomic: CCAGACACTGATGAGAGGAACCAGATGgtagcaacca ... tgcctatcagTTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGCGACAAA
EST: gi|211164169|gb|FL132744.1|FL132744
EST:     CCAGACACTGATGAGAGGAACCAGATG                         TTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGTGACAAA
genomic: CCAGACACTGATGAGAGGAACCAGATGgtagcaacca ... tgcctatcagTTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGCGACAAA
EST: gi|211164175|gb|FL132750.1|FL132750
EST:     CCAGACACTGATGAGAGGAACCAGATG                         TTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGTGACAAA
genomic: CCAGACACTGATGAGAGGAACCAGATGgtagcaacca ... tgcctatcagTTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGCGACAAA
EST: gi|211164176|gb|FL132751.1|FL132751
EST:     CCAGACACTGATGAGAGGAACCAGATG                         TTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGTGACAAA
genomic: CCAGACACTGATGAGAGGAACCAGATGgtagcaacca ... tgcctatcagTTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGCGACAAA
EST: gi|18660490|gb|BM500889.1|BM500889
EST:     CTATGACTGACACATCTACAGATCCAGACACTGATGAGAGGAACCAGATG                         TTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGCGACAAA
genomic: CTATGACTGACACATCTACAGATCCAGACACTGATGAGAGGAACCAGATGgtagcaacca ... tgcctatcagTTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGCGACAAA
EST: gi|211164172|gb|FL132747.1|FL132747
EST:     CCAGACACTGGCTGAGAGGAACCAGATG                         TTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGTGACAAA
genomic: CCAGACACT-GATGAGAGGAACCAGATGgtagcaacca ... tgcctatcagTTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGCGACAAA
EST: gi|211164171|gb|FL132746.1|FL132746
EST:     CCAGACACTGATGAGAGGAACCAGATG                         TTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGTGACAAA
genomic: CCAGACACTGATGAGAGGAACCAGATGgtagcaacca ... tgcctatcagTTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGCGACAAA
EST: gi|211164170|gb|FL132745.1|FL132745
EST:     CCAGACACTGATGAGAGGAACCAGATG                         TTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGTGACAAA
genomic: CCAGACACTGATGAGAGGAACCAGATGgtagcaacca ... tgcctatcagTTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGCGACAAA
EST: gi|211164174|gb|FL132749.1|FL132749
EST:     CCAGACACTGATGAGAGGAACCAGATG                         TTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGTGACAAA
genomic: CCAGACACTGATGAGAGGAACCAGATGgtagcaacca ... tgcctatcagTTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGCGACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatttatcagcatatactaaagtataccagtttactaattatctgcctatcagTTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGCGACAAATCAAGGGACAAACTAGATCAGAAG
                                  tactaat  putative branch site (score: 1)
                                           tctgcct  putative PPT
             atatactaaagtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgcttatctttttgtaacatttatgttgtgcttatctttttgtaacatttatcagcatatactaaagtataccagtttactaattatctgcctatcagTTTGAACAAGGACTTGTTGCTGTCCCCACAGCATCTGATTCTAGCGACAAATCAAGGGACAAACTAGATCAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA