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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttccttcctgctcctttcttcgtgcatttcctcgaccgcctggtgggcgtgtgtgctgatgccctgctttttcctctgcagAAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG

Basic information

species Zea mays
transcript GRMZM2G081462_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081462_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 1
-------gttcct-tcctgctcctttcttcgtgcatttcctcgaccgcctggtgggcgtgtg-----------tgctgatgccctgctttttcctctgcagAAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG
       ||| |  ||  ||| ||| |||  ||||||||  ||| | |||||||||||  ||           |  |  | |  |  |||||  | |||||||||| ||||| || ||||| |||||||||||||||||||| ||||| ||||| || || |||||
gttcgtagttgcagtctagcttcttgctt--tgcatttcaccgagcacctggtgggcgcttgctaatgctcctttttttttctttttttttttttttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG
















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|78112391|gb|DV530785.1|DV530785
EST:     CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG
genomic: CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttccttcct ... tcctctgcagAAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG
EST: gi|149097284|gb|EE183107.2|EE183107
EST:     CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG
genomic: CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttccttcct ... tcctctgcagAAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG
EST: gi|84969707|gb|DW468136.1|DW468136
EST:     CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG
genomic: CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttccttcct ... tcctctgcagAAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG
EST: gi|76016942|gb|DT944112.1|DT944112
EST:     CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG
genomic: CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttccttcct ... tcctctgcagAAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG
EST: gi|15323476|gb|BI478494.1|BI478494
EST:     CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG
genomic: CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttccttcct ... tcctctgcagAAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG
EST: gi|211408498|gb|FL069298.1|FL069298
EST:     CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG
genomic: CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttccttcct ... tcctctgcagAAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG
EST: gi|50325243|gb|CO520369.1|CO520369
EST:     CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG
genomic: CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttccttcct ... tcctctgcagAAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG
EST: gi|78107168|gb|DV525586.1|DV525586
EST:     CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAG                         AAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG
genomic: CCGAGTTCTCCGGCTTCCTCCTCTACAAGGAGCTCGGCCGCAGGCTCAAGgttccttcct ... tcctctgcagAAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctcgaccgcctggtgggcgtgtgtgctgatgccctgctttttcctctgcagAAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG
                           tgctgat  putative branch site (score: 3)
                                 tgccctgctttttcct  CT-rich tract
                                         ttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttccttcctgctcctttcttcgtgcatttcctcgaccgcctggtgggcgtgtgtgctgatgccctgctttttcctctgcagAAAACCAACCCGGTCGTGGCGGAGATCTTCTCGCTCATGTCAAGGGACGAGGCGCGCCATGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG