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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaagatctataaaactgtgttgcaccattcagaactgtcaaaattctcttgttccattgaacaatttagtacttacttaaatccattatctcag

Basic information

species Oryza sativa
transcript LOC_Os01g04814.4
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G126860_T01 (Zea mays), 5'ss of exon 4
GGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtt-taagaagatctataaaactgtgttgcacc--attcagaactgtcaaaat--------------tctcttgttccattgaaca--atttagtacttacttaaatccattatctcag
|||||||| ||||||||||| ||||| || ||||||||||| || || |||||||||||||| |||||||||  || || |        ||  | |||||    ||  |||  ||  ||||                |  || |    |  ||||   |||||| |||    | || |||| |  |||
GGTGTTGGTCATAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAGgttacaaaaaaaaaccacgtaccattttgcattgtatatagatttgcaaaaacaaaaagggaatgtccccattatcttgtgaaacactgtttagttctttggcatattcattgttgcag

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G088834_T01 (Zea mays), 5'ss of exon 4
GGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaagatctataaaa----ctgtgttgcaccattcagaactgtcaaaattctcttgttccattgaacaatttagtacttacttaaatccattatctcag
|||||||| || |||||||| ||||| || ||||||||||| || || |||||||||||||| |||||||||  | || |  |    ||    | ||  || |        ||||  | |   | |||       |  ||  |        ||    ||||  ||  |     
GGTGTTGGTCACAATGATGATAAAGTTCTTGTTCTTGCTGCCACGAATACGCCATATGCTCTGGACCAGgttacaaaaaacttgccgaatattccgtcctgaagatgatgcaactagctagggtatctgtgcaagtcaaattagcccaagtttgaccaaatttatagtg----

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA12G09300.1 (Glycine max), 5'ss of exon 4
GGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaagatctataaaactgtgttgcaccattcagaactgtcaaaattctcttgttccattgaacaatttagtacttacttaaatccattatctcag
|||||||| || |||||| | ||||| || ||||| || |||||||| || || |||||||||||||||||  ||||||| | |||   |||| || |    || |    | |  |           || || | |     |  |  ||| | || |   | ||  |||
GGTGTTGGACACAATGATCAGAAAGTTCTTGTTCTAGCAGCTACAAATACACCTTATGCTCTAGACCAGgt--aagaaga-caatagttctgt-ttactttttttatttttattgag----------tcaatgggatgccgttttggttaatcaactt-gtaattgcag

upper sequence: LOC_Os01g04814.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA11G19120.1 (Glycine max), 5'ss of exon 4
GGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgttt-aagaagatctataaaactgtgttgcaccattcagaactgtcaaaattctcttgttccattgaacaatttagtacttacttaaatccattatctcag
||||| || || |||||| | ||||| || |||||||| |||||||| || || |||||||||||||||||   ||||| ||   |     |   |      ||   ||         || || |  ||  ||| | ||| || ||| || |                  
GGTGTGGGACACAATGATCAGAAAGTTCTTGTTCTTGCAGCTACAAATACACCTTATGCTCTAGACCAGgtaagaagaaaatagttctgtttacttatttttatcgtgattcaatgggatactgt--tttgattaatcaactt-gtaattgcag----------------

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|58594912|gb|CF993220.1|CF993220
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGA-GGG                         GCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCGCTACCCGACCTG
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
EST: gi|300215967|gb|HO088593.1|HO088593
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG                         GCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCGCTACCCGACCTG
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
EST: gi|33381146|gb|CF196489.1|CF196489
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTNNNCCAG                         GCTGTGCGCCGGCGCTTTGATAA-CGTAT
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTAT
EST: gi|58588110|gb|CF986418.1|CF986418
EST:     ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG                         GCTGTGGGCCGGCGCTTTGATAAACGTATTTACATTCCGCTACCCGACCTG
genomic: ACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG
EST: gi|313080751|gb|HO213548.1|HO213548
EST:     ACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAG                         GCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCGCTACCCGACCTG
genomic: ACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaag ... attatctcagGCTGTGCGCCGGCGCTTTGATAAACGTATTTACATTCCACTACCCGACCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGTTGGCCATAATGATGACAAAGTACTGGTTCTTGCTGCTACAAACACGCCATATGCTCTAGACCAGgtttaagaagatctataaaactgtgttgcaccattcagaactgtcaaaattctcttgttccattgaacaatttagtacttacttaaatccattatctcag

- - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - GCTGCT