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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtacattacatcatgtcatgaagtccacacaaagtatgcaatcaatcagtctcagtccacataaagtatgcaatcaatcattctcccacagtagttcttgaagaactcacttgatgtcctcatctttttttttctaacagGGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAGAGTGTAAATGACATTCACAAAAGGGGTGGAACTATTCTTGGATCATCTC

Basic information

species Zea mays
transcript GRMZM2G443985_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 5
gtaaagtacattacatcatgtcatgaagtccacacaaagtatgcaatcaatcagtctcagtccacataaagtatgcaatcaatcattctcccacagtagttcttgaagaactcacttgatgtcctcatctttttttttctaacagGGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAGAGTGTAAATGACATTCACAAAAGGGGTGGAACTATTCTTGGATCATCTC
                                    |  |    ||   |||| |  || |  ||| ||  || | ||   |  ||  |   |  | ||  ||    |   ||   | || |  |  ||| | ||||||  |||||||||||| ||||| ||||||||| | || |||||   ||||| ||||||||||||||| |||||||||||||||||||||||| |||||||  |||| |
------------------------------------atatggaaaaaggatcaatgacatt--acaaaagctaagaaaattaaaatg-taatattggagcact----gtcttcctctaattttgttttctgtgtttttc--acagGGTGGGTATAGAGGTTTCTATGCTTGTAACACCATTGACTTGAGTCCAAAGAGTGTAAACGACATTCACAAAAGGGGTGGAACTGTTCTTGGGACATCAC
















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|211132978|gb|FL170883.1|FL170883
EST:     TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAG                         GGTGGGTACAGAGGCTTCTATGCTCGCAACACCATCACCTTGACTCCAAAG
genomic: TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAGgtaaagtaca ... tttctaacagGGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG
EST: gi|148972520|gb|EE023481.2|EE023481
EST:     TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAG                         GGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG
genomic: TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAGgtaaagtaca ... tttctaacagGGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG
EST: gi|13557855|gb|BG549211.1|BG549211
EST:     TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTTTTATTCAG                         GGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG
genomic: TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAGgtaaagtaca ... tttctaacagGGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG
EST: gi|76921243|gb|DV168509.1|DV168509
EST:     CACCAAGATACTTGGGATTCAG                         GGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG
genomic: CACCAAGATACTTGGGATTCAGgtaaagtaca ... tttctaacagGGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG
EST: gi|211132969|gb|FL170874.1|FL170874
EST:     TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAG                         GGTGGGTACAGAGGCTTCTATGCTCGCAACACCATCACCTTGACTCCAAAG
genomic: TATGTGGCTTATCTGACATGTATGGTGTCACCAAGATACTTGGGATTCAGgtaaagtaca ... tttctaacagGGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccacagtagttcttgaagaactcacttgatgtcctcatctttttttttctaacagGGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAGAGTGTAAATGACATTCACAAAAGGGGTGGAACTATTCTTGGATCATCTC
                             tgtcctcatctttttt  CT-rich tract
                                    atctttttttttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtacattacatcatgtcatgaagtccacacaaagtatgcaatcaatcagtctcagtccacataaagtatgcaatcaatcattctcccacagtagttcttgaagaactcacttgatgtcctcatctttttttttctaacagGGTGGGTACAGAGGCTTCTATGCTCGCAATACCATCACCTTGACTCCAAAGAGTGTAAATGACATTCACAAAAGGGGTGGAACTATTCTTGGATCATCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA