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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatcactgagttctgatttgtttgaaatatggttgataatacactccaaagattcttaaactatatcataatctattgcag

Basic information

species Oryza sativa
transcript LOC_Os01g34620.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g34620.5 (Oryza sativa), 5'ss of exon 4
lower sequence: AC208327.4_FGT002 (Zea mays), 5'ss of exon 5
GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatcactgagttctgatttgtttgaaatatggttgataatacactccaaagattcttaaactatatcataatctattgcag
||||||||||||||||||||| |||||||||||||||||| ||||||  |||| | |||||| ||||||||  |||| ||||  ||| |  ||||||||||||| ||| | || | |  |   |||   |   | | |||   ||| ||        | | |||| || |||  | ||  ||| |||
GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTTCAGCAATATGgtaagttagctctaattagtagattgcaggctgttttgtttcaaatgca-----ggtagttttaagctctat-gttattgatttcag

upper sequence: LOC_Os01g34620.5 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G880300_T02 (Zea mays), 5'ss of exon 4
GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatcactgagt------tc------tgatttgtttgaaatatggttgataata-----cactccaaagattcttaaactatatcataatctattgcag
||||||||||||||||||||| |||||||||||||||||| ||||||  |||| | |||||| ||||||||  |||| ||||  ||| || ||||||||||||| ||  | || | |      ||      ||||||||||  |||   | | ||| ||     ||||    | ||| |||| || |||  | ||  ||| |||
GATATCAAGGAGAACCCAGTCTTGATCTACATGAAGGGTTTTCCTGAGTCTCCAATGTGTGGCTTCAGTGCACTGGCTGTTAAGGTCTTCCAGCAATATGgtaagttggctctaattagtagatcgcaggatgatttgtttcgaatgcaggtaatagtaaatgacactttttaaatt-ttaagctctat-gttattgatttcag
















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|33808808|gb|CF330289.1|CF330289
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|218489064|gb|FG948407.1|FG948407
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|58675402|gb|CK064089.1|CK064089
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|218500313|gb|FG954965.1|FG954965
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|38478580|gb|CF962713.1|CF962713
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGT
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGT
EST: gi|33662134|gb|CF293101.1|CF293101
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|218505071|gb|FG947171.1|FG947171
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|58693371|gb|CK082058.1|CK082058
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|33680954|gb|CF309193.1|CF309193
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|86596721|gb|CI286634.1|CI286634
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|218483000|gb|FG956128.1|FG956128
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatcactgagttctgatttgtttgaaatatggttgataatacactccaaagattcttaaactatatcataatctattgcag

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