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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgattacttgttagggcagctctactctgcttttgtcttcactgcggatgagtgtagtctcgggtgcttggtacaatattgaagtaattggtgtg...

Basic information

species Zea mays
transcript GRMZM5G820996_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G820996_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g33920.1 (Oryza sativa), 5'ss of exon 2
GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgattacttgttagggcagctctactctgcttttgt-cttcactgcggatgagtgtagtctcgggtgcttggtacaatattg-aagtaattggtgtg-
|||||| |||||||||||| ||||| ||||||||||||||||| || |||||||||||||||||||||||||||||||||||||| |||  |  | |  |||  ||    |       |||  || |||     |  |  |  |  || | |  |  || | | | | | |    |||  || 
GTGGGAGGCTTGTGTACCAGTACACGAAGAAGAGGGCGAGCGGGCCGAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagcgat-gcgcgatgcggcttcttcttttattcgctgtattttactttattttgggat--ttccgcggggctattatagtgtcgcatgcggatggattgt

upper sequence: GRMZM5G820996_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G05740.1 (Glycine max), 5'ss of exon 2
GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgattacttgttagggcagctctactctgcttttgtcttcactgcggatgagtgtagtctcgggtgcttggtacaatattgaagta--attggtgtg
|||||||||| || || ||    |||||||||||||| ||||| ||||||||||||||||| || |||| ||| ||||||||| |   |   ||  |    ||  | |  ||| ||||| | ||   |     | |||||      |     ||  |  ||| ||    ||  |    ||| 
GTGGGAAGCTCGTTTATCAGACTACCAAGAAGAGGGCCAGCGGACCCAAGTGCCCCGTCACTGGCAAGAGGATTCAGGGGgtgcgctttctgttactctttcaatttt-ttcttcttttttgttgtgtaattttcagtgttcggctgttcattttttttaatgttactttatgaacattgt-

upper sequence: GRMZM5G820996_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G11920.1 (Glycine max), 5'ss of exon 2
GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgattacttgttagggcagctcta-ctctgcttttgtcttcactgcggatgagtgtagtctcgggtgcttggtacaatattgaagtaattggtgtg
|||||||||| || || ||   ||||||||||||||| ||||| ||||||||||||||||| || |||| ||| ||||||||| |   |   ||  |    ||  | |  |||| ||||| | ||   |     | |||||  | | |   | ||  |   || |  |  |  ||  | | 
GTGGGAAGCTCGTTTATCAGACCACCAAGAAGAGGGCCAGCGGGCCCAAGTGCCCCGTCACTGGCAAGAGGATTCAGGGGgtgcgctttctgttactctttcaattttttctcttcttttttgttgtgtaattttcagtgttctgttgttggttttcttttatttcaagttcctttattt-

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|211533043|gb|FL043886.1|FL043886
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|30088131|gb|CB886336.1|CB886336
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|15589458|gb|BI674074.1|BI674074
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|211352603|gb|FL470915.1|FL470915
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|211533048|gb|FL043891.1|FL043891
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|31405585|gb|CD484317.1|CD484317
EST:     GGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: GGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|60348609|gb|DN215582.1|DN215582
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTTTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|31405586|gb|CD484318.1|CD484318
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|211530048|gb|FL043882.1|FL043882
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTDCAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|211533047|gb|FL043890.1|FL043890
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCMCCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|30306493|gb|CD001166.1|CD001166
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|60357248|gb|DN224221.1|DN224221
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|26557730|gb|CA829965.1|CA829965
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|60395053|gb|DN227922.1|DN227922
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|16927550|gb|BM080619.1|BM080619
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|211533046|gb|FL043889.1|FL043889
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTATCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|60345851|gb|DN212824.1|DN212824
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|60354426|gb|DN221399.1|DN221399
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
EST: gi|30087140|gb|CB885348.1|CB885348
EST:     AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGG                         ATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgatt ... atatctctagATCCCCCACTTGAGACCTGCCGAGTACAAGAGGTCCAGGTTGTCTAGGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGGAAGCTTGTGTACCAATACACCAAGAAGAGGGCGAGCGGTCCCAAGTGCCCCGTCACCGGGAAGAAGATCCAGGGGgtgagtgattacttgttagggcagctctactctgcttttgtcttcactgcggatgagtgtagtctcgggtgcttggtacaatattgaagtaattggtgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG