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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCCCCTTCTACCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaacatcattgtggctttaacattcagggacggtgtggtctagctgttgaaacattttatcccatcatttggcctttcag

Basic information

species Zea mays
transcript GRMZM2G022777_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022777_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g55260.1 (Oryza sativa), 5'ss of exon 4
----AAGCCCCTTCTACCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaacatcattgtggctttaacattcagggacggtgtggtctagctgttgaaacattttatcccatcatttggcctttcag
    |||||||| |||||||| |||||||||||||||||||||||||| ||||||||||||||| ||||||  ||   |||       ||  | |   ||| | |      | | ||  ||||   || |  ||    |  ||   |||||||
CCAGAAGCCCCTCCTACCTTCGTTTGAGTCAGCTGAAATGCGTAATCTTGCAGAGACATTGTTGCGgtaattcaagattcacaa-actttcgaaaaataggaaagcacaaatttggccattgac-tatatattcttgcc--ttcatctttcag
















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|22472534|gb|BU037014.1|BU037014
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|76281419|gb|DV020987.1|DV020987
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|91876817|gb|EB406774.1|EB406774
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|78106806|gb|DV525224.1|DV525224
EST:     CCTTCATTTGAGTCAGCCGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|149035101|gb|EE155087.2|EE155087
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|30307202|gb|CD001875.1|CD001875
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|211165539|gb|FL456882.1|FL456882
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|211305004|gb|FL154239.1|FL154239
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAA
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAA
EST: gi|78121929|gb|DV540313.1|DV540313
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|110487038|gb|EE012240.1|EE012240
EST:     CTTCATTTGAGTCAGCTGAAATGCGTAATCTCCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CTTCATTTGAGTCAGCTGAAATGCGTAATCTC-GCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|148963213|gb|EE014191.2|EE014191
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|71297616|gb|DR784759.1|DR784759
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|211307018|gb|FL154240.1|FL154240
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAA
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAA
EST: gi|78109695|gb|DV528111.1|DV528111
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|76280583|gb|DV020151.1|DV020151
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|30705707|gb|CD058888.1|CD058888
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|149080059|gb|EE169077.2|EE169077
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|67021064|gb|CO449813.1|CO449813
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|148963079|gb|EE014036.2|EE014036
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|211307022|gb|FL154244.1|FL154244
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCC-AGATGTGAAATGGGAGAGCATC
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATC
EST: gi|8367772|gb|BE050717.1|BE050717
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|149106054|gb|EE291707.2|EE291707
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|31355569|gb|CD439926.1|CD439926
EST:     CAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|76933170|gb|DV173349.1|DV173349
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|211305000|gb|FL154235.1|FL154235
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAG
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAG
EST: gi|148933119|gb|EC876754.2|EC876754
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|148995361|gb|EE034575.2|EE034575
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|31355560|gb|CD439917.1|CD439917
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
EST: gi|211131749|gb|FL468282.1|FL468282
EST:     CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAG                         GGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT
genomic: CCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaa ... ggcctttcagGGATATTATTCGCGGGAGCCCAGATGTGAAATGGGAGAGCATCAAAGGACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCCCCTTCTACCTTCATTTGAGTCAGCTGAAATGCGTAATCTCGCAGAGACATTGTTGAGgtaatctaaacatcattgtggctttaacattcagggacggtgtggtctagctgttgaaacattttatcccatcatttggcctttcag

- - - - - - - - - - - - TCAGCT
- - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - AGCTGA