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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGGGCCTGTCCCCGTGGTACGACAACCTATGCCGCCCTGTCACAGACTTGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACGgtaatcctccgtttcaaccttttgcttcgcatctgcatagttgcccaatcattcctgaccatgtcctcaacacgatgcag

Basic information

species Zea mays
transcript GRMZM2G134256_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134256_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g70170.1 (Oryza sativa), 5'ss of exon 2
CCAGGGCCTGTCCCCGTGGTACGACAACCTATGCCGCCCTGTCACAGACTTGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACGgtaatc--ctccgtttcaaccttttgct---tcgcatctg--catagttgcccaatc---attcctgaccatgtcctcaacacgatgcag
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CCAGGGTCAGTCCCCGTGGTACGACAACCTCTGCCGTCCTGTCACCGATTTGCTGCCCCTTATTGGCAGCGGCGTCCGTGGAGTCACCAGCAACCCATCAgtacgctacactacttatttcttttgctctcttgcaccttgttctgaatctgcaatcctcattgctgactgtgtccctatggcaatgcag
















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|32831538|gb|CD971216.1|CD971216
EST:     TGCTGCCCATTATCGCCAGCGG-GTCCGTGGAGTCACCAGCAACCCAACG                         ATTTTCCAAAAGGCCATTTCATCGTCCAGCGCATATGATGATCAGTTCAAG
genomic: TGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACGgtaatcctcc ... cacgatgcagATTTTCCAAAAGGCCATTTCATCGTCCAGCGCATATGATGATCAGTTCAAG
EST: gi|32840664|gb|CD980345.1|CD980345
EST:     TGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACG                         ATTTTCCAAAAGGCCATTTCATCGTCCAGCGCATATGATGATCAGTTCAAG
genomic: TGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACGgtaatcctcc ... cacgatgcagATTTTCCAAAAGGCCATTTCATCGTCCAGCGCATATGATGATCAGTTCAAG
EST: gi|8367313|gb|BE050258.1|BE050258
EST:     TGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACG                         ATTTTCCAAAAGGCCATTTCATCGTCCAGCGCATATGATGATCAGTTCAAG
genomic: TGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACGgtaatcctcc ... cacgatgcagATTTTCCAAAAGGCCATTTCATCGTCCAGCGCATATGATGATCAGTTCAAG
EST: gi|32841693|gb|CD981374.1|CD981374
EST:     TGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACG                         ATTTTCCAAAAGGCCATTTCATCGTCCAGCGCATATGATGATCAGTTCAAG
genomic: TGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACGgtaatcctcc ... cacgatgcagATTTTCCAAAAGGCCATTTCATCGTCCAGCGCATATGATGATCAGTTCAAG
EST: gi|110505274|gb|EE017595.1|EE017595
EST:     TGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACG                         ATTTTCCAAAAGGCCATTTCATCGTCCAGCGCATATGATGATCAGTTCAAG
genomic: TGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACGgtaatcctcc ... cacgatgcagATTTTCCAAAAGGCCATTTCATCGTCCAGCGCATATGATGATCAGTTCAAG
EST: gi|32839772|gb|CD979453.1|CD979453
EST:     TGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACG                         ATTTTCCAAAAGGCCATTTCATCGTCCAGCGCATATGATGATCAGTTCAAG
genomic: TGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACGgtaatcctcc ... cacgatgcagATTTTCCAAAAGGCCATTTCATCGTCCAGCGCATATGATGATCAGTTCAAG
EST: gi|32865467|gb|CF005149.1|CF005149
EST:     TGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACG                         ATTTTCCAAAAGGCCATTTCATCGTCCAGCGCATATGATGATCAGTTCAAG
genomic: TGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACGgtaatcctcc ... cacgatgcagATTTTCCAAAAGGCCATTTCATCGTCCAGCGCATATGATGATCAGTTCAAG
EST: gi|32848855|gb|CD988536.1|CD988536
EST:     TGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACG                         ATTTTCCAAAAGGCCATTTCATCGGCCAGCGCATATGATGATCAGTTCAAG
genomic: TGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACGgtaatcctcc ... cacgatgcagATTTTCCAAAAGGCCATTTCATCGTCCAGCGCATATGATGATCAGTTCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGGGCCTGTCCCCGTGGTACGACAACCTATGCCGCCCTGTCACAGACTTGCTGCCCATTATCGCCAGCGGCGTCCGTGGAGTCACCAGCAACCCAACGgtaatcctccgtttcaaccttttgcttcgcatctgcatagttgcccaatcattcctgaccatgtcctcaacacgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG