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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttcttgcttccacaacaggggtcattgtaccacatgttccagccccttaaaaccatgttaaccttttacacagCAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCGATTCACCCTACTCAATGGAGGCCCGGAGTAGG

Basic information

species Zea mays
transcript GRMZM2G003096_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003096_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g07090.1 (Oryza sativa), 3'ss of exon 8
-------gtaaatttcttgcttccacaacaggggtcattgtaccacatgttccagccccttaaaa-------ccatgttaa---------ccttttacacagCAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCGATTCACCCTACTCAATGGAGGCCCGGAGTAGG
       |||||| |||   ||    |   |||| ||    || ||||||||||| ||    |||       || | | ||           |||| ||||||||||||| | || ||||||||||| || || || ||||||||||  || ||||||||||||||||||||||| |||||| ||
gtaagtggtaaatatctcagttttgaattgggggccaccaaac-acatgttccagtcctcccaaattccaatccttctgaaagtttgatgttttttccacagCAAAAGCACTAGCAGAGCTTGCAAGGAAGCATTCAGTGGATGTCACCTTTGATTCACCCTACTCAATGGAGGCTCGGAGTCGG
















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|50334525|gb|CO529651.1|CO529651
EST:     CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTG                         CAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
genomic: CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTGgtaaatttct ... ttttacacagCAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
EST: gi|89249663|gb|DY621449.1|DY621449
EST:     CCAAGAGATTGTTTCCATAATTTTTGAGTCGCCAAGTGTAGATGAAGCTG                         CAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
genomic: CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTGgtaaatttct ... ttttacacagCAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
EST: gi|211439719|gb|FL188857.1|FL188857
EST:     CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTG                         CAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
genomic: CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTGgtaaatttct ... ttttacacagCAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
EST: gi|16378003|gb|BI992233.1|BI992233
EST:     CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTG                         CAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
genomic: CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTGgtaaatttct ... ttttacacagCAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
EST: gi|211439722|gb|FL188860.1|FL188860
EST:     CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTG                         CAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
genomic: CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTGgtaaatttct ... ttttacacagCAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
EST: gi|211152123|gb|FL081697.1|FL081697
EST:     CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTG                         CAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
genomic: CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTGgtaaatttct ... ttttacacagCAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
EST: gi|211322726|gb|FL462750.1|FL462750
EST:     CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTG                         CAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
genomic: CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTGgtaaatttct ... ttttacacagCAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
EST: gi|211439720|gb|FL188858.1|FL188858
EST:     CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTG                         CAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
genomic: CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTGgtaaatttct ... ttttacacagCAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
EST: gi|211537751|gb|FL446842.1|FL446842
EST:     CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTG                         CAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
genomic: CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTGgtaaatttct ... ttttacacagCAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
EST: gi|211439718|gb|FL188856.1|FL188856
EST:     CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTG                         CAAAAGCATTGGCGGASSTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
genomic: CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTGgtaaatttct ... ttttacacagCAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
EST: gi|76281783|gb|DV021351.1|DV021351
EST:     CCAAGAGATTGTTTCCATAATTTTTGAGTCGCCAAGTGTAGATGAAGCTG                         CAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG
genomic: CCAAGAGATTGTTTCCATAATTTCTGAGTCGCCAAGTGTAGATGAAGCTGgtaaatttct ... ttttacacagCAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtcattgtaccacatgttccagccccttaaaaccatgttaaccttttacacagCAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCGATTCACCCTACTCAATGGAGGCCCGGAGTAGG
                                     tgttaac  putative branch site (score: 2)
                                           ccttttac  CT-rich tract
                            ttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttcttgcttccacaacaggggtcattgtaccacatgttccagccccttaaaaccatgttaaccttttacacagCAAAAGCATTGGCGGAGCTTGCAAGAAAACACTCGGTGGATGTCAGATTCGATTCACCCTACTCAATGGAGGCCCGGAGTAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG