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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCCTTTGGCATTTTACAAAGGCTTCCTGCCAAACTTTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaaagctgaagagagagtggaagtatttgagcatgttaaatccaatattaacacattgtctgttgatcttgtcag

Basic information

species Zea mays
transcript GRMZM2G000510_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000510_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os11g48040.1 (Oryza sativa), 5'ss of exon 8
GGCCCTTTGGCATTTTACAAAGGCTTCCTGCCAAACTTTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaa-tgaaaagctgaagaga-------gagtggaagtatttgagcatgttaaat-ccaatattaacacattgtctgttgatcttgtcag-----
|| ||| |||||||||||||||||||||| ||||||||||| ||||||||||| ||||||||||| |||||||||||| |||||||||||||    | | |||||   |       |  |  ||||    |    |    | |   ||||| |     ||  |  ||| | ||    |     
GGACCTCTGGCATTTTACAAAGGCTTCCTCCCAAACTTTGCTAGACTGGGATCATGGAATGTGATAATGTTCTTGACACTGGAGCAGgtaaagctgatatctgaatctatattgttggataaaagtgcagggatgtacgcattattaatatcattgttttcccccttgtttttacttgaacag
















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|78109061|gb|DV527478.1|DV527478
EST:     TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAG                         GTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
genomic: TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaa ... atcttgtcagGTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
EST: gi|31349105|gb|CD433462.1|CD433462
EST:     TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAG                         GTTCAAAAGCTGTTTGTGAGGAAAGCGAC
genomic: TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaa ... atcttgtcagGTTCAAAAGCTGTTTGTGAGGAAAGCGAC
EST: gi|213173050|gb|FM188194.1|FM188194
EST:     TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAG                         GTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
genomic: TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaa ... atcttgtcagGTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
EST: gi|71332542|gb|DR803240.1|DR803240
EST:     TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAG                         GTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
genomic: TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaa ... atcttgtcagGTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
EST: gi|76292714|gb|DV032282.1|DV032282
EST:     TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAG                         GTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
genomic: TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaa ... atcttgtcagGTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
EST: gi|71758598|gb|DR956535.1|DR956535
EST:     TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAG                         GTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
genomic: TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaa ... atcttgtcagGTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
EST: gi|211425383|gb|FL463585.1|FL463585
EST:     TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAG                         GTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
genomic: TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaa ... atcttgtcagGTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
EST: gi|110210924|gb|EC892821.1|EC892821
EST:     TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAG                         GTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
genomic: TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaa ... atcttgtcagGTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
EST: gi|6501109|gb|AW202482.1|AW202482
EST:     TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAG                         GTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
genomic: TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaa ... atcttgtcagGTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
EST: gi|32907582|gb|CF012395.1|CF012395
EST:     GGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAG                         GTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
genomic: GGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaa ... atcttgtcagGTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
EST: gi|71758726|gb|DR956663.1|DR956663
EST:     TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAG                         GTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
genomic: TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaa ... atcttgtcagGTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
EST: gi|4886008|gb|AI677128.1|AI677128
EST:     TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAG                         GTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
genomic: TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaa ... atcttgtcagGTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
EST: gi|211234201|gb|FK951229.1|FK951229
EST:     TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAG                         GTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
genomic: TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaa ... atcttgtcagGTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
EST: gi|69351358|gb|DR452107.1|DR452107
EST:     TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAG                         GTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC
genomic: TTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaa ... atcttgtcagGTTCAAAAGCTGTTTGTGAGGAAAGCGACAAGCTGAAGATAGAGTTTTTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCCTTTGGCATTTTACAAAGGCTTCCTGCCAAACTTTGCAAGACTGGGATCTTGGAATGTGATTATGTTCTTGACATTGGAGCAGgtaaatgaaaagctgaagagagagtggaagtatttgagcatgttaaatccaatattaacacattgtctgttgatcttgtcag

- - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG