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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttgtggctgttgttcatacttcatacttgaaagcaggcaacagtttactcagtatgcctatactaagcaactactattgtttcccttctccttttcagTTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAG

Basic information

species Zea mays
transcript GRMZM2G077844_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 2
--------gcttgtggctgttgttcatacttcatacttgaaagcaggcaacagtttactcagtatgcctatactaagcaactactattgtttc-ccttctccttttcagTTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAG
          |  |||||  |||  |    |  |||||||||   |||| |         | || || | |  | |   |      || |||   ||| |  |||  |||||||||||||  |||||||||||||||| || |||||||||||||| |||||||||| |||||| || |||||||||||||||||||||||||| |||
taatttaatttaatggct--tgtggaaggcttttacttgaaaatgggcaccca-------aataagcatgtggtgaattatggtgtttattttgtctttttttttctagTTGCTGGAGACACTGATTAAAAATTGTGGAGACTTTGTTCATATGCACGTTGCTGAGAGGGATATACTCCATGAAATGGTGAAGATAGCTAAGAAAAAG

upper sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G08790.1 (Arabidopsis thaliana), 3'ss of exon 2
gcttgtggctgttgttcatacttcatacttgaaagcaggcaacagtttactcagtatgcctatactaagcaactactattgtttcccttc--tccttttcagTTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAG
|       |   |  |  |     ||| ||      |         ||  | |  ||   | ||  |    | ||  ||  |||   ||   | ||||  |||| || |||||  | || |  |||||||| ||  || |||||||||||||||| ||||||||||| |||||| | ||||||||||| || || | ||||
gtacacaaccaatagtatt--cagatatttacttttattttcttcctttttaaaaatttatttatgagaagattaacatattttggttttgttactttgtagTTACTAGAGACAATAATAACCAATTGTGGAGAACTTATTCATATGCAAGTTGCAGAGAAGGATATACTTCATAAGATGGTGAAGATGGCCAAAAGGAAG
















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|211007985|gb|FL246230.1|FL246230
EST:     AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACG                         TTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT
genomic: AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACGgtaaatacca ... tccttttcagTTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT
EST: gi|211469270|gb|FL411606.1|FL411606
EST:     AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACG                         TTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT
genomic: AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACGgtaaatacca ... tccttttcagTTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT
EST: gi|211030018|gb|FL411237.1|FL411237
EST:     AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACG                         TTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCAT
genomic: AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACGgtaaatacca ... tccttttcagTTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCAT
EST: gi|78103934|gb|DV522352.1|DV522352
EST:     AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACG                         TTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT
genomic: AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACGgtaaatacca ... tccttttcagTTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT
EST: gi|78118618|gb|DV537002.1|DV537002
EST:     AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACG                         TTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT
genomic: AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACGgtaaatacca ... tccttttcagTTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT
EST: gi|149083221|gb|EE172499.2|EE172499
EST:     AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACG                         TTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT
genomic: AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACGgtaaatacca ... tccttttcagTTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT
EST: gi|32868858|gb|CF008540.1|CF008540
EST:     AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACG                         TTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT
genomic: AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACGgtaaatacca ... tccttttcagTTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT
EST: gi|211139498|gb|FL390012.1|FL390012
EST:     AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACG                         TTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT
genomic: AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACGgtaaatacca ... tccttttcagTTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT
EST: gi|8368846|gb|BE051791.1|BE051791
EST:     AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACG                         TTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT
genomic: AGAAACGGATTGCACACAAGAACTCAAAGGTCCAGCTTCTTGCATTAACGgtaaatacca ... tccttttcagTTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactcagtatgcctatactaagcaactactattgtttcccttctccttttcagTTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAG
                           ctactattgtttccct  CT-rich tract
               tatactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttgtggctgttgttcatacttcatacttgaaagcaggcaacagtttactcagtatgcctatactaagcaactactattgtttcccttctccttttcagTTGCTGGAGACCTTGATTAAAAATTGTGGTGATTTTGTTCATATGCAAGTTGCTGAGAAGGATATGCTTCATGAAATGGTGAAGATAGCTAAGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG