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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccacattatgttgtctaatgttgtgaggatgatacttataaaacatttcgagccggccttgtttcatttctggactaattatgtgtgtgtaatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAGTCGGTGAACGACATCCATAAGAGAGGCGGGACTGTCCTCGGAACCTCAA

Basic information

species Zea mays
transcript GRMZM2G080375_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080375_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 4
-gccacatta-tgttgtctaatgttgtgaggatgatacttataaaacatttcgagccggccttgtttcatttctggactaattatgtgtgtgtaatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAGTCGGTGAACGACATCCATAAGAGAGGCGGGACTGTCCTCGGAACCTCAA
    |   || || ||| |  |||    | | || | || || |    ||  || |   |  | |||  ||| | ||||   |     |||| | ||| |||||||||||||||||||||||||||| |||||| || ||  ||||||| || |||||||| |||||||| |||||||| |||||||| || |||||||| |
catgatgctaatgctgtttg-tgtgtaaatggtgctcctaatcagttgttgtgatcattctgtttttgttttattgacttgattctgatgtgca-tgtttagGGTGGATACAAGGGTTTCTATTCTAGAAACACCGTCGCACTGACACCGAAATCGGTGAATGACATCCACAAGAGAGGTGGGACTGTTCTTGGAACCTCCA
















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|74234373|gb|DT642287.1|DT642287
EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
EST: gi|116813643|gb|EC856113.1|EC856113
EST:     GGCGTCT-CAGCGTCGTCGGCATACAG                         GGTGGATACAA-GG-TTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: GGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
EST: gi|148940563|gb|EC885365.2|EC885365
EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
EST: gi|148941151|gb|EC886025.2|EC886025
EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTG
EST: gi|18661967|gb|BM501673.1|BM501673
EST:     TTGGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
EST: gi|33099629|gb|CF059589.1|CF059589
EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAAGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCGAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
EST: gi|76914829|gb|DV165709.1|DV165709
EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
EST: gi|149087521|gb|EE176918.2|EE176918
EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
EST: gi|76290797|gb|DV030365.1|DV030365
EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
EST: gi|149111238|gb|EE294735.2|EE294735
EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
EST: gi|76913985|gb|DV165359.1|DV165359
EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
EST: gi|78078027|gb|DV506442.1|DV506442
EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTTGT-GCGTTGACACCAAA
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACT-GTTGCGTTGACACCAAA
EST: gi|148935767|gb|EC879810.2|EC879810
EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
EST: gi|87153260|gb|DY398049.1|DY398049
EST:     TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAG                         GGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG
genomic: TTTGCGGCTTGTATGATATGTATGGCGTCTCCAGCGTCGTCGGCATAGAGgtgaggaccg ... taatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcgagccggccttgtttcatttctggactaattatgtgtgtgtaatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAGTCGGTGAACGACATCCATAAGAGAGGCGGGACTGTCCTCGGAACCTCAA
                            gactaat  putative branch site (score: 2)
                             actaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccacattatgttgtctaatgttgtgaggatgatacttataaaacatttcgagccggccttgtttcatttctggactaattatgtgtgtgtaatgtgtagGGTGGATACAAGGGTTTCTATTCTAAAAACACTGTTGCGTTGACACCAAAGTCGGTGAACGACATCCATAAGAGAGGCGGGACTGTCCTCGGAACCTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG