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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcctcggttctcgccctctcttctccgcatgcctgcagcgtattggactaaaactaactgatgtgtcggccatcgtgcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGGACCAAAGACGGGTATAATCCGCTTCTCGACGATTTCAAGAACACAAAGT

Basic information

species Zea mays
transcript GRMZM2G101217_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101217_T08 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g68390.1 (Oryza sativa), 3'ss of exon 12
-----------------------------------gtgagtcctcg-gttctcgccctctcttctccgcatgcctgcagcgtattggactaaaactaactgatgtgtcggccatcgtgcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGGACCAAAGACGGGTATAATCCGCTTCTCGACGATTTCAAGAACACAAAGT
                                    ||   ||| | || || |  |    | |  | |||   |        | ||   |      | |    |||      ||    |     |||||||| |||| ||||||||||| ||||||||  ||||| ||||||| ||||||||||| || |||||||| || || || ||||||| |||||| ||||
gtaagttcagactatttaagccagttttgttttctatgcaacctagtgtcctagttcatcttgcatcacatcttttacaaacttcggtgcactgacgagtatgatgttatttgtcaactatcgttagCTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGGACCAAAGATGGATATAATCCACTCCTTGATGATTTCAGGAACACCAAGT
















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|50337134|gb|CO532260.1|CO532260
EST:     AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATA                         CTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
genomic: AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATAgtgagtcctc ... gcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
EST: gi|93012640|gb|EB638160.1|EB638160
EST:     AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATA                         CTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
genomic: AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATAgtgagtcctc ... gcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
EST: gi|71418851|gb|DR804567.1|DR804567
EST:     AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATA                         CTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
genomic: AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATAgtgagtcctc ... gcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
EST: gi|50336105|gb|CO531231.1|CO531231
EST:     AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATA                         CTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
genomic: AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATAgtgagtcctc ... gcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
EST: gi|161587502|gb|EY961654.1|EY961654
EST:     CGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATA                         CTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
genomic: CGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATAgtgagtcctc ... gcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
EST: gi|71763051|gb|DR960988.1|DR960988
EST:     AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATA                         CTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
genomic: AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATAgtgagtcctc ... gcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
EST: gi|50325601|gb|CO520727.1|CO520727
EST:     AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATA                         CTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
genomic: AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATAgtgagtcctc ... gcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
EST: gi|76281531|gb|DV021099.1|DV021099
EST:     AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATA                         CTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
genomic: AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATAgtgagtcctc ... gcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
EST: gi|148960596|gb|EE011218.2|EE011218
EST:     AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATA                         CTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
genomic: AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATAgtgagtcctc ... gcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
EST: gi|60352980|gb|DN219953.1|DN219953
EST:     AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATA                         CTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
genomic: AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATAgtgagtcctc ... gcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
EST: gi|76924071|gb|DV169789.1|DV169789
EST:     AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATA                         CTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG
genomic: AGAAGAATCCCGGCGCATTCAAACCCGTGAAGAAGAGGAGAACGATCATAgtgagtcctc ... gcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgcagcgtattggactaaaactaactgatgtgtcggccatcgtgcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGGACCAAAGACGGGTATAATCCGCTTCTCGACGATTTCAAGAACACAAAGT
                 taaaactaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcctcggttctcgccctctcttctccgcatgcctgcagcgtattggactaaaactaactgatgtgtcggccatcgtgcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGGACCAAAGACGGGTATAATCCGCTTCTCGACGATTTCAAGAACACAAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC