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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGAGCCGAAGCGCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctcttcctctgacttgttcgggtcgaggagatagatatgtagcgcgctataataaccgacgccttcgccttcgttcgtctctgctctgcag

Basic information

species Zea mays
transcript GRMZM2G026470_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026470_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g36260.1 (Oryza sativa), 5'ss of exon 1
GTGGAGCCGAAGCGCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctcttcctctgacttgttcgg-gtcgaggagatagatatgtagcgcgctataataaccgacgccttcgccttcgttcgtctctgctctgcag---------------------------------------------------------------
                             ||||||| | ||||| ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||    |   | |  | | | |||||   ||||       |      |       |  |    ||  |  || |  |||  ||  ||  | || ||| |                                                               
-----------------------------GAACGAGAGGATCCTCTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCGTGGCACGACCTCGAGATCGGCC--CTGATGCTCCCGCCGTGTTCAACGTCgtaagtgcacgccc-tgttcttttgcatcctcctccagctccagcttaattattccgttctttgccgcccggccgctggcgatgatgacagctttgttgcgatgtgtcccgtggtggatttttggcacag

upper sequence: GRMZM2G026470_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ33488 (Selaginella moellendorffii), 5'ss of exon 1
GTGGAGCCGAAGCGCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctcttcctctgacttgttcgggtcgaggagatagatatgtagcgcgctataataaccgacgccttcgccttcgttcgtctctgctctgcag-------
                                                 || || ||    | | |||||| ||||| ||||||||||||||||| ||||||  || || ||   ||  || |   | |      | |     ||       ||      | ||||    | |  |||||   | | ||| |   |        
------------------------------------------------GCGATGGCGGACCGATTCGTCGCGGCGCATCCCTGGCACGACCTCGAAATCGgtacgc-tcgtctcgtg--ttctcttgattctcaggctgttcttgcgatcttctcacgcgatcgaccgtcttgt-ttcgtggat-tttgccccaaaaccccaag

upper sequence: GRMZM2G026470_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ27219 (Selaginella moellendorffii), 5'ss of exon 1
GTGGAGCCGAAGC--GCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctcttcctctgacttgttcgggtcgaggagatagatatgtagcgcgctataataaccgacgccttcgccttcgttcgtctctgctctgcag
| | |  ||      |||    |||   ||| ||| |||||||||| |||||||| || ||  | |||||||| ||||| ||||||||||| ||||| |||||| |  || | | |||   ||| |    || |  |   ||  | | | ||| |    | |  | | |  ||  |||| |                  
GCGAACTCGGGTTCTGCCAAAAGCCC--GCTTAACAAGCGCATCCTCTCGTCGCTCTCCCGCCGCTCCGTCGCGGCGCATCCCTGGCACGATCTCGAAATCGgtaaagct-tgcgtctttgttgcttctttcaa--atgcaggaaggaatcgctc----acacacaatgttttttccttag------------------

upper sequence: GRMZM2G026470_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ33440 (Selaginella moellendorffii), 5'ss of exon 1
GTGGAGCCGAAGC--GCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctcttcctctgacttgttcgggtcgaggagatagatatgtagcgcgctataataaccgacgccttcgccttcgttcgtctctgctctgcag
| | |  ||      |||    |||   ||| ||| |||||||||| |||||||| || ||  | |||||||| ||||| ||||||||||| ||||| |||||| |  || | | |||   ||| |    || |  |   ||  | | | ||| |    | |  | | |  ||  |||  |                  
GCGAACTCGGGTTCTGCCAAAAGCCC--GCTTAACAAGCGCATCCTCTCGTCGCTCTCCCGCCGCTCCGTCGCGGCGCATCCCTGGCACGATCTCGAAATCGgtaaagct-tgcgtctttgttgcttctttcaa--atgcaggaaggaaccgctc----acacacaatgttttttcctcag------------------

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|78121802|gb|DV540186.1|DV540186
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTCGTAAGTATCTGACGAATCCCAT
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTCGTAAGTATCTGACGAATCCCAT
EST: gi|18964261|gb|BM660905.1|BM660905
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTCGT
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTCGT
EST: gi|22490296|gb|BU050219.1|BU050219
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTCGT
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTCGT
EST: gi|19821815|gb|BQ047839.1|BQ047839
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTCGT
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTCGT
EST: gi|18964037|gb|BM660771.1|BM660771
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTCGT
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTCGT
EST: gi|87153912|gb|DY398701.1|DY398701
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCG                         GTCCTGAAGCTCCGGCCGTCTTCAACGTCGT
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTCGT
EST: gi|19057948|gb|BM736615.1|BM736615
EST:     GCTGTCGCGGAGGTCCGTCGCCGCGCACCCC-GGCACGACCTCGAGATCG                         GTCCTGAAGC-CCGGCCGTCTTCAACGTCGT
genomic: GCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctct ... tgctctgcagGTCCTGAAGCTCCGGCCGTCTTCAACGTCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGAGCCGAAGCGCCGGGCGCCGCGGCTGAACGAGCGCATCCTGTCGTCGCTGTCGCGGAGGTCCGTCGCCGCGCACCCCTGGCACGACCTCGAGATCGgtgagcctcttcctctgacttgttcgggtcgaggagatagatatgtagcgcgctataataaccgacgccttcgccttcgttcgtctctgctctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC