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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTTTAGCAAACATGGTTGTTTCACTTGCTGATCAGCCCTCCACAAGGCTGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAGgtctgtcctatcattcgtattctgcgaagttattttacaaatgccccaacaatatatgtaatcttttgaacttttccctttctacgcag

Basic information

species Zea mays
transcript GRMZM2G045331_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045331_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g37790.1 (Oryza sativa), 5'ss of exon 9
GTGTTTTAGCAAACATGGTTGTTTCACTTGCTGATCAGCCCTCCACAAGGCTGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAGgtctgtcctatcattcgtattctgcgaagttattttac--aaatgccccaacaatatatgtaatcttttgaacttttccctttctacgcag
||||||||||||||||||| |||||||||||||| ||||| ||||||||| ||||||||||||| || || ||||||||  |||||||||| ||  | |||||||| ||  |||| || | ||   || |||||||||  ||||   |  |    | | |  || ||||   ||   |    |||| ||||
GTGTTTTAGCAAACATGGTAGTTTCACTTGCTGAGCAGCCTTCCACAAGGTTGCTGAAGCACATTATCCGATGTTACCTTAGGCTGTCAGACAATTCCAGgtctgtgctgacatttgtgtgctatcaaattattttacttaaatattctga----acaggctattttttt--ctacgcggcgtctatgcag

upper sequence: GRMZM2G045331_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g52340.1 (Oryza sativa), 5'ss of exon 9
GTGTTTTAGCAAACATGGTTGTTTCACTTGCTGATCAGCCCTCCACAAGGCTGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAGgtctgtcctatcattcgtattctgcgaagttattttac--aaatgccccaacaatatatgtaatcttttgaacttttccctttctacgcag
||||||||||||||||||| |||||||||||||| ||||| ||||||||| ||||||||||||| || || ||||||||  |||||||||| ||  | |||||||| ||  |||| || | ||   || |||||||||  ||||   |  |    | | |  || ||||   ||   |    |||| ||||
GTGTTTTAGCAAACATGGTGGTTTCACTTGCTGAGCAGCCTTCCACAAGGTTGCTGAAGCACATTATCCGATGTTACCTTAGGCTGTCAGACAATTCCAGgtctgtgctgccatttgtgtgctatcaaattattttacttaaatattctga----acaggctattttttt--ctacgcggcgtctatgcag
















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|32868505|gb|CF008187.1|CF008187
EST:     CTGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAG                         GGCTTGTGCTGCATTGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGAC
genomic: CTGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAGgtctgtccta ... ttctacgcagGGCTTGTGCTGCATTGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGAC
EST: gi|78091208|gb|DV519582.1|DV519582
EST:     CTGCGGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAG                         GGCTTGTGCTGCATGGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGAC
genomic: CTGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAGgtctgtccta ... ttctacgcagGGCTTGTGCTGCATTGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGAC
EST: gi|13149745|gb|BG320067.1|BG320067
EST:     TGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCCTAG                         GGCTTGTGCTGCATTGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGA
genomic: TGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAA-CCCTAGgtctgtccta ... ttctacgcagGGCTTGTGCTGCATTGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGA
EST: gi|88746243|gb|DY530384.1|DY530384
EST:     CTGCGGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAG                         GGCTTGTGCTGCATTGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGAC
genomic: CTGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAGgtctgtccta ... ttctacgcagGGCTTGTGCTGCATTGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGAC
EST: gi|31352432|gb|CD436789.1|CD436789
EST:     CTGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAG                         GGCTTGTGCTGCATTGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGAC
genomic: CTGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAGgtctgtccta ... ttctacgcagGGCTTGTGCTGCATTGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGAC
EST: gi|76281455|gb|DV021023.1|DV021023
EST:     AGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAG                         GGCTTGTGCTGCATTGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGAC
genomic: AGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAGgtctgtccta ... ttctacgcagGGCTTGTGCTGCATTGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGAC
EST: gi|71445882|gb|DR826932.1|DR826932
EST:     CTGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAG                         GGCTTGTGCTGCATTGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGAC
genomic: CTGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAGgtctgtccta ... ttctacgcagGGCTTGTGCTGCATTGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGAC
EST: gi|78074797|gb|DV503231.1|DV503231
EST:     CTGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAG                         GGCTTGTGCTGCATTGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGAC
genomic: CTGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAGgtctgtccta ... ttctacgcagGGCTTGTGCTGCATTGCAGAGCTGCCTTCCAGACATGCTCAAAGATGGGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTTTAGCAAACATGGTTGTTTCACTTGCTGATCAGCCCTCCACAAGGCTGCTGAAGCACATCATTCGTTGTTACCTCCGGCTGTCAGATAACCCTAGgtctgtcctatcattcgtattctgcgaagttattttacaaatgccccaacaatatatgtaatcttttgaacttttccctttctacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC