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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGACCTCGACCGCTTCGGCAAGGCCGTCAAGCTCACTGCCTTCAATCCTTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctccttccccacctaaacacgcaggctcgctgcgagatgattttgttctgacttctgacccgggctctggcgcttcctttcccgtggccag

Basic information

species Zea mays
transcript GRMZM2G110233_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110233_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g22880.1 (Oryza sativa), 5'ss of exon 1
CTGGACCTCGACCGCTTCGGCAAGGCCGTCAAGCTCACTGCCTTCAATCCTTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctc-cttccccacctaaacacgcaggctcgctgcgagatgattt-tgttctgacttctgacccgggctctggcgcttc----ctttcccgtggccag
 | ||||||||||||||||||||||||||||||||| | |||||||  || |||||||| ||||| ||||| ||||||||||||||||| ||||| ||||||   ||| | | |   |     | |    ||  |||  |    ||||  || |    || ||       | | |     |      |  | ||| |  |||
GTCGACCTCGACCGCTTCGGCAAGGCCGTCAAGCTCGCCGCCTTCACCCCCTTCTCCTCCGCCGTGGACGCCCTCAACCAGTGCAACGCCATCTCCGAAGgtcctctcgcgttcttgcgccgccgccgccgccagctcaggcgggattcgtgcttcttctccttttttttgttttttttttctgacgccattccgcgtgcag
















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|26557755|gb|CA829990.1|CA829990
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|211325180|gb|FL364049.1|FL364049
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|211049346|gb|FL323595.1|FL323595
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|20803431|gb|BQ294481.1|BQ294481
EST:     TTTCTCCTCTGCCGCCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|26559620|gb|CA831855.1|CA831855
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|30031584|gb|CB833435.1|CB833435
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|84980362|gb|DW530711.1|DW530711
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCCATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|29543698|gb|CB604078.1|CB604078
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|30087070|gb|CB885278.1|CB885278
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|29130402|gb|CB381106.1|CB381106
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|213177969|gb|FM186729.1|FM186729
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCCATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|14717697|gb|BI245347.1|BI245347
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCCATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|22715748|gb|BU197940.1|BU197940
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|5296088|gb|AI782963.1|AI782963
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|15427341|gb|BI543163.1|BI543163
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCCATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|211213156|gb|FL322467.1|FL322467
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|31557980|gb|CD527192.1|CD527192
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|15100491|gb|BI396282.1|BI396282
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCCATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|24934830|gb|CA453048.1|CA453048
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|28910643|gb|CB331541.1|CB331541
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|211009565|gb|FL317969.1|FL317969
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|28873547|gb|CB329522.1|CB329522
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|87157139|gb|DY401928.1|DY401928
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|32913216|gb|CF018028.1|CF018028
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCCATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|84980547|gb|DW530896.1|DW530896
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCCATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|29130368|gb|CB381072.1|CB381072
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
EST: gi|24934839|gb|CA453057.1|CA453057
EST:     TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAG                         GAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC
genomic: TTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctcct ... ccgtggccagGAATCATGACCGATGAGTTGAGGAGCTTCCTGGAGCTGAACCTGCCGAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGACCTCGACCGCTTCGGCAAGGCCGTCAAGCTCACTGCCTTCAATCCTTTCTCCTCTGCCGTCGACGCGCTCAACCAGTGCAACGCTATCTCTGAAGgttggctccttccccacctaaacacgcaggctcgctgcgagatgattttgttctgacttctgacccgggctctggcgcttcctttcccgtggccag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG