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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGCGAGCGCCGCCTCCCCTCCCTCGCTCCGTGAGGTCCTCGCCGGCGACGAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctctgtcactctccccttcccttcctgctgcgcggaactgaagaccccaaaccctaatgcgagttatctctattcggatctgccccaattgcga...

Basic information

species Zea mays
transcript GRMZM2G030902_T04
intron # 1
splice site 5'
intron type U2

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|211347523|gb|FL007072.1|FL007072
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
EST: gi|31664299|gb|CD573024.1|CD573024
EST:     GAG-GCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
EST: gi|211345133|gb|FL007069.1|FL007069
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
EST: gi|211345131|gb|FL007067.1|FL007067
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
EST: gi|211345128|gb|FL007064.1|FL007064
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
EST: gi|211347524|gb|FL007073.1|FL007073
EST:     GAGTGCCGCCG-CCGTTTCCATGTTTTTTCCTTCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
EST: gi|211345132|gb|FL007068.1|FL007068
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
EST: gi|211345126|gb|FL007062.1|FL007062
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
EST: gi|211345123|gb|FL007059.1|FL007059
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
EST: gi|6564152|gb|AW231774.1|AW231774
EST:     GAGTGCTGCCGCCCGTTTCCATGTATTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAGGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
EST: gi|211345130|gb|FL007066.1|FL007066
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
EST: gi|211345122|gb|FL007058.1|FL007058
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
EST: gi|211345125|gb|FL007061.1|FL007061
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTATTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
EST: gi|211345134|gb|FL007070.1|FL007070
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
EST: gi|211345127|gb|FL007063.1|FL007063
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTTGGTAACTTTGACGCAAGGTGTTCAAGAAATTTAAGC
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGC-TGGTAAC-TTGACGCAAGGTGTTCAAGAAATTTAAGC
EST: gi|211345135|gb|FL007071.1|FL007071
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
EST: gi|211345129|gb|FL007065.1|FL007065
EST:     GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAG                         ATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA
genomic: GAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctct ... caactttcagATCTAGTGAAGGCTGGTAACTTGACGCAAGGTGTTCAAGAAATTTAAGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGCGAGCGCCGCCTCCCCTCCCTCGCTCCGTGAGGTCCTCGCCGGCGACGAGTGCCGCCGCCCGTTTCCATGTTTTTTCCGCCGATTAGTGTCCACCAGgtacgcctctgtcactctccccttcccttcctgctgcgcggaactgaagaccccaaaccctaatgcgagttatctctattcggatctgccccaattgcga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcccc