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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccacaatagccttttggggcagatagttttaacaaatgtgttccttcttatggctttattaagttctatttttcattctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA

Basic information

species Zea mays
transcript GRMZM2G079538_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 4
gtaagccacaatagccttttggggcagatagt-tttaacaaatgtgttccttcttatggctttattaagttctatttttcattctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA
||||||  ||    | || || |||||| | |  || | |||  ||||||| |      | ||||  | |  | || |||||     ||||||||| || |||| |||||||| || |||||||||||||||||||||||||||||||||||||||||||| ||||
gtaagctgcacctcctttatgaggcagacaatgctttataaaattgttcctgc------ccttatcgattgtttttgttcat-----atagGAGACCAGGTTGAAGCTGTTGTCCCTTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTGAAGA
















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|148950981|gb|EC896624.2|EC896624
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|211169879|gb|FL077608.1|FL077608
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|211325989|gb|FL407943.1|FL407943
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|211233035|gb|FK998528.1|FK998528
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACNAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|148943959|gb|EC889039.2|EC889039
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|31355469|gb|CD439826.1|CD439826
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|31355590|gb|CD439947.1|CD439947
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|149015063|gb|EE044815.2|EE044815
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|149009740|gb|EE041651.2|EE041651
EST:     TAATCCCTCTCCATACCACGTTTGGAGTACGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCC
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCC
EST: gi|5343075|gb|AI795485.1|AI795485
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|78103875|gb|DV522298.1|DV522298
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|148958216|gb|EC904424.2|EC904424
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|148991485|gb|EE033000.2|EE033000
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|149081048|gb|EE170148.2|EE170148
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|211169872|gb|FL077601.1|FL077601
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|148931436|gb|EC874404.2|EC874404
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|31358640|gb|CD442997.1|CD442997
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|211230977|gb|FK998519.1|FK998519
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|148978727|gb|EE026283.2|EE026283
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|149014456|gb|EE044070.2|EE044070
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|149003557|gb|EE038930.2|EE038930
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|211321201|gb|FL380429.1|FL380429
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|31353408|gb|CD437765.1|CD437765
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|211169881|gb|FL077610.1|FL077610
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACNAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|67033243|gb|CO461992.1|CO461992
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
EST: gi|211169620|gb|FL396011.1|FL396011
EST:     TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACG                         GAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG
genomic: TAATCCCTCTCCATACCAAGTTTGGAGTAGGTCATTTGCTTCAGACAACGgtaagccaca ... ttctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaaatgtgttccttcttatggctttattaagttctatttttcattctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA
 ttttaac  putative branch site (score: 2)
                                 ttctatttttcattct  putative PPT
                        tttattaagttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccacaatagccttttggggcagatagttttaacaaatgtgttccttcttatggctttattaagttctatttttcattctatatagGAGACAAGTTTGAGGCTGTTGTGCCCTTCATGGGTGAATCTGTAACTGATGGAACTCTTGCTAACTTCTTAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA