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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttatcctgtactacatttcacagtttttacagtgcactgttacttttaacccctcttccgtatctgcatcattgagcaatggtcttgttactcagGGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACATTGTTGCTATGAAGCGCTCTCGGCCCAAAGTTCTTCGTCTGAATCTGGTG

Basic information

species Oryza sativa
transcript LOC_Os05g51190.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51190.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G142068_T01 (Zea mays), 3'ss of exon 3
gtaatgttatcctgtactacatttcacagtttttacagtgcactgttacttttaacccctcttccgtatctgcatcattgagcaatggt-cttgttactcagGGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACATTGTTGCTATGAAGCGCTCTCGGCCCAAAGTTCTTCGTCTGAATCTGGTG
             ||| |  |   ||||  |||||     | |   | || ||    |  || | | |  | | || |  |  |||  |  |||||  |||||||| |||| || || ||||| || |||||||| || || || |||||||| || |||||||||||||| |  |||||||||||||| ||||| ||||||
-------------gtaatggaac-cacacattttatcagtctc---tcctcttggttcaactgctgcaaattcgtcttataataataatatttgttcatcagGGAGCTGAAGCACGAGGAGAAGCGCTGCATGGAGGAGCTGCAGTGCAACATCGTGGCTATGAAGCGCTCCCAACCCAAAGTTCTTCGGCTGAACCTGGTG

upper sequence: LOC_Os05g51190.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G20750.1 (Glycine max), 3'ss of exon 3
-----------------------------gtaatgttatcctgtactacatttcacagtttttacagtgcac-tgttacttttaacccctcttccgtatctgcatcattgagcaatggtcttgttactcagGGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACATTGTTGCTATGAAGCGCTCTCGGCCCAAAGTTCTTCGTCTGAATCTGGTG
                             |  | | | |||| |  ||    | | | ||  |    |  || | ||   ||||     || | |  |  |  |   ||| |   | | ||| ||   |||  || | |||||||| || || || |||||||||||||| || || |||||||| | ||||||||| |||| ||| ||||| || ||  ||||| || | 
gtaatagtctctcttatattttcctcactgagaagct-tcctattgtaaccataaaacttgatgatatctacatttttggtttattgtttcgttctgagattaaattttgtgttgttgccttctt-tgcagACAGCTTAAACATGAGGAAAAGCGATGCATGGAAGAACTGCAGTGTAACATTGTAGTTATGAAGCGTTCTCAGCCTAAAGTACTGCGCTTGAATTTGATT

upper sequence: LOC_Os05g51190.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv09s0002g02420.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------------------------------------gtaatgttatcctgtactacatttcacagtttttacagtgca-ctgttacttttaacccctcttccgtatctgcatcattgagcaatggtcttgttact--cagGGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACATTGTTGCTATGAAGCGCTCTCGGCCCAAAGTTCTTCGTCTGAATCTGGTG
                                                                               || |  | |      ||    |  |    |||    || || | ||||  |        || |   | |   | |  || |    |  |  |||||    |||| || | |||||||| || ||| | |||||||| || || |||||||||||||| | |||||||||||| |  || |||||||| ||  ||||| |||| 
gtaatatactctttctaatttttccataaaaatgtttttatttatttatttattttcatttccctcctgggaattcctttatttctctgtcaagctgttgtctattaatttcttggttcagcagttatgtccttattttcattactcttcccttggttaaaagttacttgtgttatgtgcagGCAGCTCAAACATGAGGAAAAATGCTGCATGGAGGAGCTGCAATGCAACATTGTGGTTATGAAGCGCTCCCAACCTAAAGTTCTCCGCTTGAATTTGGTT

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|58679376|gb|CK068063.1|CK068063
EST:     GTGGCTACTGAATCAAAGCGTGCCCAAGCAAGCTGGGTTGTGCTAGACAA                         GGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACAT
genomic: GTGGCTACTGAATCAAAGCGTGCCCAAGCAAGCTGGGTTGTGCTAGACAAgtaatgttat ... tgttactcagGGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACAT
EST: gi|58681849|gb|CK070536.1|CK070536
EST:     GTGGCTACTGAATCAAAGCGTGCCCAAGCAAGCTGGGTTGTGCTAGACAA                         GGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACAT
genomic: GTGGCTACTGAATCAAAGCGTGCCCAAGCAAGCTGGGTTGTGCTAGACAAgtaatgttat ... tgttactcagGGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACAT
EST: gi|58679423|gb|CK068110.1|CK068110
EST:     GTGGCTACTGAATCAAAGCGTGCCCAAGCAAGCTGGGTTGTGCTAGACAA                         GGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACAT
genomic: GTGGCTACTGAATCAAAGCGTGCCCAAGCAAGCTGGGTTGTGCTAGACAAgtaatgttat ... tgttactcagGGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACAT
EST: gi|58662467|gb|CK051153.1|CK051153
EST:     GTGGCTACTGAATCAAAGCGTGCCCAAGCAAGCTGGGTTGTGCTAGACAA                         GGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACAT
genomic: GTGGCTACTGAATCAAAGCGTGCCCAAGCAAGCTGGGTTGTGCTAGACAAgtaatgttat ... tgttactcagGGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACAT
EST: gi|38476078|gb|CF960211.1|CF960211
EST:     GTGGCTACTGAATCAAAGCGTGCCCAAGCAAGCTGGGTTGTGCTAGACAA                         GGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACAT
genomic: GTGGCTACTGAATCAAAGCGTGCCCAAGCAAGCTGGGTTGTGCTAGACAAgtaatgttat ... tgttactcagGGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACAT
EST: gi|86877342|gb|CI311548.1|CI311548
EST:     GTGGCTACTGAATCAAAGCGTGCCCAAGCAAGCTGGGTTGTGCTAGACAA                         GGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACAT
genomic: GTGGCTACTGAATCAAAGCGTGCCCAAGCAAGCTGGGTTGTGCTAGACAAgtaatgttat ... tgttactcagGGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttttaacccctcttccgtatctgcatcattgagcaatggtcttgttactcagGGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACATTGTTGCTATGAAGCGCTCTCGGCCCAAAGTTCTTCGTCTGAATCTGGTG
   ttttaac  putative branch site (score: 2)
                                          tcttgtt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgttatcctgtactacatttcacagtttttacagtgcactgttacttttaacccctcttccgtatctgcatcattgagcaatggtcttgttactcagGGAGTTGAAACATGAAGAGAAACGTTGCATGGAAGAACTTCAATGCAACATTGTTGCTATGAAGCGCTCTCGGCCCAAAGTTCTTCGTCTGAATCTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC