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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttaccttccctatccacgaatcctccggcgatatggccccttgttccttctcctgacgggtctcatctcctgtagTGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCGACTACACGCGGTACCG

Basic information

species Zea mays
transcript GRMZM2G121022_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121022_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g23360.1 (Oryza sativa), 3'ss of exon 1
gtgagcttaccttcc--ctatccacgaatcctccggcgatat-------ggccccttgttccttctcc------tgacgggtctcatctcct----gtagTGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCGACTACACGCGGTACCG---------------------------------
||| ||||  |||||  |  ||  |  |  | |||  | |         |  |||| ||| ||  |||       | ||| |||| ||||||    | |||||| ||||||||||||||||||||||||||||| || ||||||||  ||||||||||||||||| |                                 
gtgggcttctcttcctcccctctccccactccccgatggttccacgaccgatccctagttgctgatccgggcgccgccggttctcctctcctcctcgcagTGCTGGAGCTCATGAGGGAGGCGCAGATGCAGCACGGCCTCCGCCACGGCGACTACACGCGGTACAGGTGCGCGCTCCCGGACTTCCTACCAGATCTGTC
















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|211123457|gb|FL321151.1|FL321151
EST:     CGACTCCTCCGTCGCCGAGGAGAAGCCGGCCATCAGATTCTCCATCAACG                         TGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCG
genomic: CGACTCCTCCGTCGCCGAGGAGAAGCCGGCCATCAGATTCTCCATCAACGgtgagcttac ... tctcctgtagTGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCG
EST: gi|31356396|gb|CD440753.1|CD440753
EST:     CGACTCCTCCGTCGCCGAGGAGAAGCCGGCCATCAGATTCTCCATCAACG                         TGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCG
genomic: CGACTCCTCCGTCGCCGAGGAGAAGCCGGCCATCAGATTCTCCATCAACGgtgagcttac ... tctcctgtagTGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCG
EST: gi|149106635|gb|EE188528.2|EE188528
EST:     CGACTCCTCCGTCGCCGAGGAGAAGCCGGCCATCAGATTCTCCATCAACG                         TGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCG
genomic: CGACTCCTCCGTCGCCGAGGAGAAGCCGGCCATCAGATTCTCCATCAACGgtgagcttac ... tctcctgtagTGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCG
EST: gi|211414496|gb|FL334087.1|FL334087
EST:     CGACTCCTCCGTCGCCGAGGAGAAGCCGGCCATCAGATTCTCCATCAACG                         TGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCG
genomic: CGACTCCTCCGTCGCCGAGGAGAAGCCGGCCATCAGATTCTCCATCAACGgtgagcttac ... tctcctgtagTGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCG
EST: gi|78087914|gb|DV516307.1|DV516307
EST:     CGACTCCTCCGTCGCCGAGGAGAAGCCGGCCATCAGATTCTCCATCAACG                         TGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCG
genomic: CGACTCCTCCGTCGCCGAGGAGAAGCCGGCCATCAGATTCTCCATCAACGgtgagcttac ... tctcctgtagTGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCG
EST: gi|211528870|gb|FL340834.1|FL340834
EST:     CGACTCCTCCGTCGCCGAGGAGAAGCCGGCCATCAGATTCTCCATCAACG                         TGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCG
genomic: CGACTCCTCCGTCGCCGAGGAGAAGCCGGCCATCAGATTCTCCATCAACGgtgagcttac ... tctcctgtagTGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCG
EST: gi|211399643|gb|FL347347.1|FL347347
EST:     CGACTCCTCCGTCGCCGAGGAGAAGCCGGCCATCAGATTCTCCATCAACG                         TGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCG
genomic: CGACTCCTCCGTCGCCGAGGAGAAGCCGGCCATCAGATTCTCCATCAACGgtgagcttac ... tctcctgtagTGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctccggcgatatggccccttgttccttctcctgacgggtctcatctcctgtagTGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCGACTACACGCGGTACCG
                              tcctgac  putative branch site (score: 2)
                                        tctcatctcct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcttaccttccctatccacgaatcctccggcgatatggccccttgttccttctcctgacgggtctcatctcctgtagTGCTTGAGCTCATGAGGGAGGCGCAGATGCAGCATGGTCTCCGCCAGAGCGACTACACGCGGTACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG