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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctgaacgatgtcttctcgtgtccagtttttcttttggggttgagtttgtgactgaagtacctactacctacgtgtcttgtgctttcatttagat...

Basic information

species Zea mays
transcript GRMZM2G059381_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059381_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 18
AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctgaacgatgtcttctcgtgtccagtttttcttttggggttgagtttgtgactgaagtacctactacctacgtgtcttgtgctttcatttagat---
 ||||| ||||||||||| ||||| ||| ||||||||||||| || ||   |||| | ||||| || ||||| |||||||| |||||||||    | |  ||      |    |  | | | | |||     |        || ||   | || ||| |||      |    || ||||  ||  ||   
GAGAGATGTCATTGATGAAGATGGATGGCTACATACTGGAGATATTGGGACGTGGTTACCTGGTGGTCGTCTCAAAATTATTGATAGgtaagatagcatcattctaattaaactataatctatattt---aataagaaacatggcttctgaacttaccacccgttattaaattgatttctgtttaatata

upper sequence: GRMZM2G059381_T03 (Zea mays), 5'ss of exon 5
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 5'ss of exon 18
AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctgaacgatgtcttctcgtgtccagtttttcttt---tggggttgagtttgtgactgaagtacctactacctacgtgtcttgtgctt-tcatttagat
 | |||||| |||||||| ||||| ||| | || |||||||| |||||| |||||||||| ||||| |||||||||||||| || ||||    |  ||       |  | ||   ||| | ||  ||   |    |  | | | |   ||    ||  |  |    | |   |  | ||  | ||  | | 
GAAAGAGGTGATTGATGAAGATGGATGGCTTCACACTGGAGATATAGGTCTGTGGCTGCCGGGAGGACGTCTAAAAATTATTGACAGgttttccaaaaaatcacttgattgttatcagctgtttcttcactaaaatcaaatctct---tggctcacaaagaataagcctacttcttactgatgatacaaa-

upper sequence: GRMZM2G059381_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 18
AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctgaacgatgtc-ttctcgtgtccagttttt-------cttttgggg-------ttgagttt---gtgactgaagtacctactacctacgtgtcttg-tgctttcatttagat-------------------------------------------------------------------------------
 |||||||| |||||||| ||||| ||| | ||||| |||||||||||||| ||| | |||||||| || ||||| || || |||||||||||    || || || || | ||   ||||| ||        |  |   |       |  |||||    ||||| || |  ||  ||  | | | ||||| | || | |||| | |                                                                               
GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAGgtaaag----accatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactg-tatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgacag

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|33090935|gb|CF050929.1|CF050929
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|87153602|gb|DY398391.1|DY398391
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|19350747|gb|BM895279.1|BM895279
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|60395514|gb|DN228384.1|DN228384
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|58030032|gb|CX725459.1|CX725459
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|93283329|gb|EB675593.1|EB675593
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|32847207|gb|CD986888.1|CD986888
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|211308069|gb|FL216534.1|FL216534
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctgaacgatgtcttctcgtgtccagtttttcttttggggttgagtttgtgactgaagtacctactacctacgtgtcttgtgctttcatttagat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG