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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgtagtggcatcagatctggaattctcagaaatggttatcttatctcatgatttctttaagcacttggtttttttagaagatagtggattgaacattgtttcttgaaatttagttgtttttttccgtatacttctccaaacaggcctgcttgactacattatgtgcatattgtgattctcagCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC

Basic information

species Zea mays
transcript GRMZM5G819212_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G819212_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g47930.1 (Oryza sativa), 3'ss of exon 2
gtcagtgtagtggcatcagatctggaattctcagaaatggttatcttatctcatgatttctttaagcacttggtttttttagaagatagtggattgaacattgtttcttg--aaatttagttgtttttttccgtatacttctcca-aacaggcctgcttgactacattatgtgcatattgtgattctcagCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC
                                                                                          ||  |  |  ||  |    |  ||| ||   | |||||||| |  ||   ||  | ||| |  |    ||| | |||| ||||| |  | ||||| | || |||||||||||| || || ||||||||| ||||||||||||||||||||||||||||| 
------------------------------------------------------------------------------------------gggctttattttaatggaagacaaacttgtgtttttttttctgagtaaaactatagaactgatcgatatgagtgcattttgtgctttatttgattttaagAAGAGGAAGTCAATGACTTGGGAGTCAATGTGGCACTATCCATGCTAAAATTTTACAAAA

upper sequence: GRMZM5G819212_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g15970.3 (Oryza sativa), 3'ss of exon 2
gtcagtgtagtggcatcagatctggaattctcagaaatggttatcttatctcatgatttctttaagcacttggtttttttagaagatagtggattgaacattgtttcttga-aatttagttgtttttttccgtatacttctcca-aacaggcctgcttgactacattatgtgcatattgtgattctcagCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC
                                                                                         |||  |  |  ||  |    || ||  | ||  |||||||| |  ||   ||  | ||| |  |     || | |||| ||||  | |||||||| | || |||||||||||| || || ||||||||  ||||||||||||||||||||||||||||| 
----------------------------------------------------------------------------------------ttgggctttattttaatggaagacaaacttgtgttttttttctgagtaaaactatagaactgatcgatacgagtgcattttgtgttt-ttgtgattttaagAAGAGGAAGTCAATGACTTGGGAGTCAACGTGGCACTATCCATGCTAAAATTTTACAAAA

upper sequence: GRMZM5G819212_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g15970.4 (Oryza sativa), 3'ss of exon 2
gtcagtgtagtggcatcagatctggaattctcagaaatggttatcttatctcatgatttctttaagcacttggtttttttagaagatagtggattgaacattgtttcttgaaatttagttgtttttttccgtatacttctcca-aacaggcctgcttgactacattatgtgcatattgtgattctcagCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC
                                                                                          || || |   |  |       ||  | ||  |||||||| |  ||   ||  | ||| |  |     || | |||| ||||  | |||||||| | || |||||||||||| || || ||||||||  ||||||||||||||||||||||||||||| 
------------------------------------------------------------------------------------------ggctttattttaatggaagacaaacttgtgttttttttctgagtaaaactatagaactgatcgatacgagtgcattttgtgttt-ttgtgattttaagaagAGGAAGTCAATGACTTGGGAGTCAACGTGGCACTATCCATGCTAAAATTTTACAAAA

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|211290851|gb|FL314522.1|FL314522
EST:     GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAG                         -AG-G-AAGTCAAAGATTTTRGAGTCAATATGGCACTATCCATGCTAAAAT
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... tgattctcagCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT
EST: gi|211269504|gb|FL311290.1|FL311290
EST:     GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACG-A-                         -AGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... tgattctcagCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT
EST: gi|211390914|gb|FL318343.1|FL318343
EST:     GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAG                         CAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... tgattctcagCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT
EST: gi|211135169|gb|FL439581.1|FL439581
EST:     GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTACTGAAGACGAAG                         CAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... tgattctcagCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT
EST: gi|211286457|gb|FL309059.1|FL309059
EST:     GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAG                         CAGAAGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAA
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... tgattctcagCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT
EST: gi|6918525|gb|AW400055.1|AW400055
EST:     GTGGAGGAAGGNTCCGGCATGGCGACTCCACTGTGGTGCTGAAGACGAAG                         CAGAGGAAGGCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... tgattctcagCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT
EST: gi|33467473|gb|CF244522.1|CF244522
EST:     GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAG                         CAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... tgattctcagCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT
EST: gi|211336107|gb|FL367026.1|FL367026
EST:     GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTACTGAAGACGAAG                         CAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... tgattctcagCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT
EST: gi|37381402|gb|CF627583.1|CF627583
EST:     GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAG                         CAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT
genomic: GTGGAGGAAGGTTCCGGCATGGCGACTCCACTGTGTTGCTGAAGACGAAGgtcagtgtag ... tgattctcagCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacttctccaaacaggcctgcttgactacattatgtgcatattgtgattctcagCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC
                    gcttgac  putative branch site (score: 4)
                                                ttctc  putative PPT
                           tacattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgtagtggcatcagatctggaattctcagaaatggttatcttatctcatgatttctttaagcacttggtttttttagaagatagtggattgaacattgtttcttgaaatttagttgtttttttccgtatacttctccaaacaggcctgcttgactacattatgtgcatattgtgattctcagCAGAGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG