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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattatgtatatttggataaaaggggggcattttaaagtttttttttgtatgtctagttgtggttatgttcattatttcatttggtttctttcttgaagGTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAATGGAACAAGCAACTATTCAGTGCCTCGGTTGTCTCAAGTCAAAAATACCT

Basic information

species Zea mays
transcript GRMZM2G118467_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118467_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g27230.1 (Oryza sativa), 3'ss of exon 2
ttattatgtatat--ttggataaaaggggggcattttaaagtttttttttgtatgtctagttgtggttatgttca-ttatttcattt-ggtttctttcttgaagGTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAATGGAACAAGCAACTATTCAGTGCCTCGGTTGTCTCAAGTCAAAAATACCT
| || ||| | |    | | |     || ||| |||    |||  |||    |  || ||||    |    ||   ||||    ||| | |||  | |||||||||| || ||||| || || || |||||| | ||||||||||| |||||||||||||||||||| ||||||||||| |||||  |||||||||||||||||
tgataatgcaaaacactagctctttaggtggccttt----gttggtttcaacacttccagttccaatgggatttggttataatgttttgatttactccttgaagGTACCGTATACAAAGTGATCGAAAAGTCGCAATCTGCAGTGTACATCCAATGGAACAAGCAACAATTCAGTGCCTTGGTTGCGTCAAGTCAAAAATACCT
















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|149111796|gb|EE190949.2|EE190949
EST:     GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATG                         GTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
genomic: GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATGgtaagtagct ... tttcttgaagGTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
EST: gi|71763927|gb|DR961864.1|DR961864
EST:     GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGAACAGATG                         GTATCGCATACAGAGCGACCGGAAAGTCCCTATCTG
genomic: GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATGgtaagtagct ... tttcttgaagGTATCGCATACAGAGCGACCGGAAAGTCCCTATCTG
EST: gi|148983394|gb|EE029390.2|EE029390
EST:     GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATG                         GTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
genomic: GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATGgtaagtagct ... tttcttgaagGTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
EST: gi|71763924|gb|DR961861.1|DR961861
EST:     GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATG                         GTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
genomic: GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATGgtaagtagct ... tttcttgaagGTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
EST: gi|31354963|gb|CD439320.1|CD439320
EST:     GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATG                         GTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
genomic: GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATGgtaagtagct ... tttcttgaagGTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
EST: gi|31355095|gb|CD439452.1|CD439452
EST:     GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATG                         GTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
genomic: GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATGgtaagtagct ... tttcttgaagGTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
EST: gi|31353161|gb|CD437518.1|CD437518
EST:     GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATG                         GTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
genomic: GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATGgtaagtagct ... tttcttgaagGTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
EST: gi|149111287|gb|EE294785.2|EE294785
EST:     GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATG                         GTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
genomic: GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATGgtaagtagct ... tttcttgaagGTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
EST: gi|148934306|gb|EC878332.2|EC878332
EST:     GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATG                         GTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
genomic: GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATGgtaagtagct ... tttcttgaagGTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
EST: gi|5268397|gb|AI770361.1|AI770361
EST:     GCGG-ACAGATG                         GTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
genomic: GCGGTACAGATGgtaagtagct ... tttcttgaagGTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
EST: gi|149111055|gb|EE294552.2|EE294552
EST:     GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATG                         GTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT
genomic: GATGTCCCCGAAACCGCGCCCGCTGATGGCCAGTTCATGCGGTACAGATGgtaagtagct ... tttcttgaagGTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtatgtctagttgtggttatgttcattatttcatttggtttctttcttgaagGTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAATGGAACAAGCAACTATTCAGTGCCTCGGTTGTCTCAAGTCAAAAATACCT
                                    tttggtttctttctt  CT-rich tract
                   ttatgttcattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattatgtatatttggataaaaggggggcattttaaagtttttttttgtatgtctagttgtggttatgttcattatttcatttggtttctttcttgaagGTATCGCATACAGAGCGACCGGAAAGTCCCTATCTGCAGTGTGCATCCAATGGAACAAGCAACTATTCAGTGCCTCGGTTGTCTCAAGTCAAAAATACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA