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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggagatcttgaaacataagtttaaacttacagatgtttctgccgagctttctaacttaggttaaaatttctgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGTTGGAGGACCATCAGCCCCCAGAAGGCTTTGTTGTTGCAAGAGGTCTGTA

Basic information

species Zea mays
transcript GRMZM2G162175_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162175_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g06790.2 (Oryza sativa), 3'ss of exon 6
gtaagtggagatcttgaaacataagtttaaacttacagatgtttctgccgagctttctaacttaggttaaaatttctgccta--------ccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGTTGGAGGACCATCAGCCCCCAGAAGGCTTTGTTGTTGCAAGAGGTCTGTA
||| || ||||||||  ||| | |  ||    |||||     | |||       ||||||||   |         | | |          |||||||||||||||| ||| ||| ||||| |  | ||| ||||||||||||| |||||||||||||| || ||||| ||||||||||| || |||||| ||||
gtatgtagagatcttataacttgaacttgttattacac-cactgctgagcgctgttctaactcccgccccccaccccgtccgatattcctccagTTGTTTTGCCTGGTGAAATAAATAGCGCAGAAGTAATTTGGTTGGAGGAATTGGAGGACCATCAACCTCCAGAGGGCTTTGTTGTCGCGAGAGGTTTGTA
















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|149078130|gb|EE166879.2|EE166879
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|110200615|gb|EC882512.1|EC882512
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|213173437|gb|FM193786.1|FM193786
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCNACCTG                         TTGTTTTGCCTGCT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCT
EST: gi|110954112|gb|EE174164.1|EE174164
EST:     ATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: ATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|91052877|gb|EB163295.1|EB163295
EST:     TGGGGGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|211331596|gb|FL468865.1|FL468865
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|50329440|gb|CO524566.1|CO524566
EST:     TTCATACTTCCGAAAGTTTCAGATGAATCAGCCCCCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTTTCAGGTAGTTTGGTTGGAGGAGT
genomic: TTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|149096943|gb|EE182742.2|EE182742
EST:     TTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|101382864|gb|EB813486.1|EB813486
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|76925182|gb|DV170317.1|DV170317
EST:     TGGGGGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|12971808|gb|BG267668.1|BG267668
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|113809067|gb|DW930297.1|DW930297
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGG
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGG
EST: gi|78119800|gb|DV538184.1|DV538184
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|29130501|gb|CB381205.1|CB381205
EST:     TGGGCGACCCTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCCCCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|149013589|gb|EE043058.2|EE043058
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|83278650|gb|DV942658.1|DV942658
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|166447313|gb|EG142167.1|EG142167
EST:     TGGGCGACACTGTTCATACTTCCGAAAATCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGC
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGC
EST: gi|4681159|gb|AI629829.1|AI629829
EST:     TGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttacagatgtttctgccgagctttctaacttaggttaaaatttctgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGTTGGAGGACCATCAGCCCCCAGAAGGCTTTGTTGTTGCAAGAGGTCTGTA
                       ttctaac  putative branch site (score: 1)
                                         tttctgcct  putative PPT
                              ttaggttaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtggagatcttgaaacataagtttaaacttacagatgtttctgccgagctttctaacttaggttaaaatttctgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGTTGGAGGACCATCAGCCCCCAGAAGGCTTTGTTGTTGCAAGAGGTCTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG