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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttctttttacatcagatgtatttttttcttcagcctcttcaccatcagatatactatgactaagacctttttctttctcttttcttgggcatctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTGGTCCCCATACTGAGTACATTATATCTCTTGATGCAGAGGACTTATCACA

Basic information

species Zea mays
transcript GRMZM2G062154_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062154_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g48370.1 (Oryza sativa), 3'ss of exon 2
------------cttctttttacatcagatgtatttttttcttcagcctcttcaccatcagatatact--atgactaagacctttttctttctcttttcttgggcatctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTGGTCCCCATACTGAGTACATTATATCTCTTGATGCAGAGGACTTATCACA
            ||  |||||  | ||  || | |    | |  | | | |||||||||| || | ||  |||| ||| |  |  || ||             | || |||||||| ||||| ||||||||||||| ||||||||||||||||| || || |||||||||||||| ||||||||  |||| |||||||| || ||| | |||||
atatttttccttctggtttttgtaccaactgcaatgccatatgga-ctttttcaccatcaaatgtgcttgatgattaatatatacttttt-------------gtatatgatagCAACTGTGGATAAAGGGAAGTTCCTCATGGCTGCTAGAAGGTTTAGACGTGGTCCCCATACCGAGTACATCGTATCCCTTGATGCTGATGACCTTTCACA

upper sequence: GRMZM2G062154_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G35920.1 (Glycine max), 3'ss of exon 2
cttctttttacatcagatgtatttttttcttcagcctcttcaccatcagatatactatgactaagacctttttctttctcttttcttgggcatc---tgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTGGTCCCCATACTGAGTACATTATATCTCTTGATGCAGAGGACTTATCACA
  || |  | || || || |   ||| ||||     | |||           |   ||   |    | || || || |||||||||    || |   ||  ||||       ||||||||||||||||  | || ||||| ||||  ||| ||||| ||||||||||||| || || || |||||||| || |||||||| ||
--tcataatgca-catattttggtttctcttttaagttttcttggatgtgcttgaaatttatgcctctttattgttactcttttctcccccacccattgccagCATTCACAGATAAAGGGAAGTTTCTGCTAGCAGCTAGGAGATATAGGTGTGGTACCCATACTGAGTATATAATTTCACTTGATGCTGATGACTTATCCCA
















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|38687992|gb|CK145023.1|CK145023
EST:     CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTG
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTG
EST: gi|19272436|gb|BM888692.1|BM888692
EST:     CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGACTT-AGGCGT
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGA-TTAAGGCGT
EST: gi|19058652|gb|BM737319.1|BM737319
EST:     CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGACTT-AGGCGT
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGA-TTAAGGCGT
EST: gi|211111224|gb|FK952889.1|FK952889
EST:     CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGA
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGA
EST: gi|74244974|gb|DT652888.1|DT652888
EST:     CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTG
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTG
EST: gi|211111223|gb|FK952888.1|FK952888
EST:     CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTG
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTG
EST: gi|211112130|gb|FK952891.1|FK952891
EST:     CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGACTTA-GGCGT
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGA-TTAAGGCGT
EST: gi|211111218|gb|FK952883.1|FK952883
EST:     CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGKGTATAAAGGGAAGTTTTCTCATGGCTGCTAGAAGA
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTT-CTCATGGCTGCTAGAAGA
EST: gi|22490929|gb|BU050852.1|BU050852
EST:     CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGACTT-AGGCGT
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGA-TTAAGGCGT
EST: gi|149040587|gb|EE046828.2|EE046828
EST:     CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTG
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTG
EST: gi|22490595|gb|BU050518.1|BU050518
EST:     CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGACTT-AGGCGT
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGA-TTAAGGCGT
EST: gi|211111222|gb|FK952887.1|FK952887
EST:     CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGACTTA-GGCGT
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGA-TTAAGGCGT
EST: gi|87152741|gb|DY397530.1|DY397530
EST:     CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGACTT-AGGCGT
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGA-TTAAGGCGT
EST: gi|74239976|gb|DT647890.1|DT647890
EST:     CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTG
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTG
EST: gi|86466002|gb|DY232375.1|DY232375
EST:     CATGCGGAATAAAAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAAAAGATTAAGGCGTG
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTG
EST: gi|71329294|gb|DR801349.1|DR801349
EST:     CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTG
genomic: CATGCGGAATAAGAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtacaa ... catctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagatatactatgactaagacctttttctttctcttttcttgggcatctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTGGTCCCCATACTGAGTACATTATATCTCTTGATGCAGAGGACTTATCACA
                     cctttttctttctctt  CT-rich tract
                       tttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttctttttacatcagatgtatttttttcttcagcctcttcaccatcagatatactatgactaagacctttttctttctcttttcttgggcatctgatagCACCTGTGTATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTAAGGCGTGGTCCCCATACTGAGTACATTATATCTCTTGATGCAGAGGACTTATCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - -tgtattt
- - - - - - - - - - - - - - cttcagc
- - - - - - - - - - - - - - - - - - - - caccatc