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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAATTCGTCGAACGCCACCCCACCCGCCCACTGCAATGGCGAGCTTCAATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgcgcgcttctgcggccgccttgccgggtgaaaaaaaacccagggttcgatttgactgggtggtgtttccgttgtctgttacag

Basic information

species Zea mays
transcript GRMZM2G180815_T01
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|50331331|gb|CO526457.1|CO526457
EST:     ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAG                         GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
genomic: ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
EST: gi|211313573|gb|FL072330.1|FL072330
EST:     ATCCCGCCGGCGCCAGCGCCGCCWACCATAATCCCAACAAATCCTTCGAG                         GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
genomic: ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
EST: gi|91878349|gb|EB408306.1|EB408306
EST:     ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAG                         GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
genomic: ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
EST: gi|71448754|gb|DR829804.1|DR829804
EST:     ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAG                         GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
genomic: ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
EST: gi|78073885|gb|DV502319.1|DV502319
EST:     ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAG                         GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
genomic: ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
EST: gi|74235195|gb|DT643109.1|DT643109
EST:     ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAG                         GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
genomic: ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
EST: gi|211313572|gb|FL072329.1|FL072329
EST:     ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAG                         GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
genomic: ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
EST: gi|88757960|gb|DY542101.1|DY542101
EST:     ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAG                         GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
genomic: ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
EST: gi|94472144|gb|EB701102.1|EB701102
EST:     ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAG                         GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
genomic: ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
EST: gi|211313574|gb|FL072331.1|FL072331
EST:     ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAG                         GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
genomic: ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
EST: gi|74234227|gb|DT642141.1|DT642141
EST:     ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAG                         GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
genomic: ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
EST: gi|71432894|gb|DR813944.1|DR813944
EST:     ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAG                         GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
genomic: ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
EST: gi|50332450|gb|CO527576.1|CO527576
EST:     ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAG                         GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
genomic: ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
EST: gi|74240564|gb|DT648478.1|DT648478
EST:     ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAG                         GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
genomic: ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
EST: gi|76930213|gb|DV172299.1|DV172299
EST:     ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAG                         GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG
genomic: ATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 119

CCAAATTCGTCGAACGCCACCCCACCCGCCCACTGCAATGGCGAGCTTCAATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG


Block sizes: 46 (upstream exon), 40 (downstream exon)
Score: 20

CCAAATTCGTCGAACGCCACCCCACCCGCCCACTGCAATGGCGAGCTTCAATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 19

CCAAATTCGTCGAACGCCACCCCACCCGCCCACTGCAATGGCGAGCTTCAATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 17

CCAAATTCGTCGAACGCCACCCCACCCGCCCACTGCAATGGCGAGCTTCAATCCCGCCGGCGCCAGCGCCGCCAACCATAATCCCAACAAATCCTTCGAGgtccgtgcgc ... tctgttacagGTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG