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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagggcattggcatgaaaattattttgatccatgtttttaagataaagttcattttgtttcacaagtttctaagcttacatttcattatttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCCATCATGATATCATCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA

Basic information

species Zea mays
transcript GRMZM2G448715_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G448715_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 5
cagggcattggcatga-aaattattttgatccatgtttttaagataaagttcattttgtttcacaagtttctaagcttacatttcattatttgt--------ttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCCATCATGATATCATCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA
       || | || | ||  | ||  ||   || |   | |   |     |||||    ||||  | |  ||| ||||     | ||||| ||        || |||||||| |||||||||||||||||||| |||||||| ||| |||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
------tttagaataacaaggtgttcagactaatataacttatgcattaaacatttc---tcacgggctattaaacttatgccactttattggtataacacttttgcagCTGGTATTGTCATTGAGGAGAAAAACTGGCCTCCATTTCTGCCACTCATCCATCATGATATCACCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA

upper sequence: GRMZM2G448715_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 5
cagggcattggcatgaaaattattttgatccatgtttttaagataaagttcattttgtttcacaagtttctaagcttacatttcattat-ttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCCATCATGATATCATCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA
  |||   |      ||  ||    | || | | ||  |   | ||     |||||   ||     ||  |   | |   | | ||||  || | |  ||||||| |||||  |||||||||| |||||||| || ||| | ||| | |||||||||||||||   ||||| || || | ||| ||||||||| |||| ||
ttgggtgcttat-caaagtttgaactcatgctttttgcttgaacaataaatatttttggtctgcttttattcttcatgtgtgtaattacattatcttacagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCATTTTTCCCAATTATCCATCATGATATCGCTAATGAAATTCCAATTCATCTTCAAAGATTGCAGTA

upper sequence: GRMZM2G448715_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G31090.1 (Glycine max), 3'ss of exon 5
--cagggcattggcatgaaaattattttgatccatgtttttaagataaagttcattttgtttcacaagtttctaagcttacatttcattatttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCCATCATGATATCATCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA
   |  | | || |   |    ||  |   |     || |    |  || || | ||    |       ||||| |     |||| |   ||||||| |||||||| |||||  |||||||||| |||||||| |||||| | ||| | ||||||||||| ||    ||||| || || | ||| ||||||| | |||||||
atgatagtactgccgaaatctatagatgtcttggaattatatgcactaattttagttctgctttggtacttcta-gtaggtattt-acattttgttttgcagCTGGAATTGTTCTTGAGGAGAAGAATTGGCCGCCTTTTTTCCCAATAATCCATCATGACATTGCTAATGAAATTCCAATTCATCTTCAAAAATTGCAATA

upper sequence: GRMZM2G448715_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 3
cagggcattggcatgaaaattattttgatccatgtttttaagataaagttcattttgtttcacaagtttctaagcttacatttcattatttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCCATCATGATATCATCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA
          | ||    | |  ||  |  |   |||  |  |   |       |  |  |   |||||    | ||||| ||  || ||  ||| |||||||| ||||| || ||||||||||||||||| ||||||   ||  |||| ||||| || ||    ||||| ||||| |  || ||||||  ||| || ||
----------gtattttgagttcttcaacac---tttacataacccaacaggagtaatgcctttagtttggtggtttacactt--tttttgtttttgcagCTGGAATTGTTATAGAGGAGAAAAATTGGCCACCTTTTTGCCCCATCATTCATCACGACATTGCAAATGAAATACCTATACATCTTCAATCAATCCAGTA

upper sequence: GRMZM2G448715_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 5
--cagggcattggcatgaaaattattttgatccatgtttttaagataaagttcattttgtttcacaagtttctaagcttacatttcattatttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCCATCATGATATCATCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA
   |   ||||        | | | |||  || |   |   || |     ||  ||||      ||| || |     | |  |||  |  |||||||  ||||||| |||||  ||||||||||||||||||| || ||  | ||| | ||||||||||||||    ||||| ||||||| ||| || ||||   |||| ||
ctaataacattatggacttattcaatttcctcaaacctccaaacaccccattagtttttccatgcaatttac--gtttcaagttttctactttgttttccagCTGGAATTGTTCTTGAGGAGAAAAATTGGCCACCATTCTTCCCAATTATCCATCATGATATTGCGAATGAAATACCGATTCATCTACAAAAGTTGCAGTA

upper sequence: GRMZM2G448715_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 4
cagggcattggcatgaaaattattttgatccatgtttttaagataaagttcatt--ttgtttcacaagtttctaagcttacatttcattatttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCCATCATGATATCATCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA
          |  ||    || |||  |||  |  |      || | ||| | |  |  |||||     |    |   || || ||||| ||| |||||||||||| |||||||| ||||||||||||||||| || ||| | || || || |||||||| ||    ||||| ||||| |  || |  || |   |||| ||
----------gtttgtctgttgtttatatcattagtgaatcaattaggttgagtagtgttttcatgcagtctacaatctaaatatcattctttctttggcagCTGGAATTGTCATAGAGGAGAAAAATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTA

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|91048315|gb|EB158733.1|EB158733
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCAAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCAAGAGgtaaatgctc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC
EST: gi|33770808|gb|CF273102.1|CF273102
EST:     GAACTAAAACAGAGAGAGGAGGCTGCAGCAAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCAAGAGgtaaatgctc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC
EST: gi|211223444|gb|FL382580.1|FL382580
EST:     GAACTAAAACGGAGAGAGGAGGCTGCA-CAAGAG                         CTGGCATTGTCAT
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCAAGAGgtaaatgctc ... tgtttggcagCTGGCATTGTCAT
EST: gi|28188216|gb|CB179826.1|CB179826
EST:     GAACTAAAACAGAGAGAGGAGGCTGCAGCAAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCAAGAGgtaaatgctc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC
EST: gi|76931490|gb|DV172743.1|DV172743
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCAAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCAAGAGgtaaatgctc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC
EST: gi|211023203|gb|FK976157.1|FK976157
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCAAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCAAGAGgtaaatgctc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC
EST: gi|37621984|gb|CF675037.1|CF675037
EST:     GAACTAAAACAGAGAGAGGAGGCTGCAGCAAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCAAGAGgtaaatgctc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC
EST: gi|211025647|gb|FK976165.1|FK976165
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCAAGAG                         CTGGCATTGTCATTGAGGAGA
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCAAGAGgtaaatgctc ... tgtttggcagCTGGCATTGTCATTGAGGAGA
EST: gi|89251197|gb|DY622983.1|DY622983
EST:     GAACTAAAACGGAGAGAGGAGGCTGCAGCAAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCAAGAGgtaaatgctc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC
EST: gi|37621886|gb|CF674939.1|CF674939
EST:     GAACTAAAACAGAGAGAGGAGGCTGCAGCAAGAG                         CTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC
genomic: GAACTAAAACGGAGAGAGGAGGCTGCAGCAAGAGgtaaatgctc ... tgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttcattttgtttcacaagtttctaagcttacatttcattatttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCCATCATGATATCATCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA
                           agcttac  putative branch site (score: 3)
                                           tttgttt  putative PPT
                              ttacatttcattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagggcattggcatgaaaattattttgatccatgtttttaagataaagttcattttgtttcacaagtttctaagcttacatttcattatttgtttggcagCTGGCATTGTCATTGAGGAGAAAAATTGGCCTCCTTTTATGCCACTCATCCATCATGATATCATCAATGAGATACCGAGTCACCTTCAAAGAATGCAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA