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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattatcactgagttctgatttgtttgaaatatggttgataatacactccaaagattcttaaactatatcataatctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC

Basic information

species Oryza sativa
transcript LOC_Os01g34620.6
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g34620.5 (Oryza sativa), 3'ss of exon 4
lower sequence: AC208327.4_FGT002 (Zea mays), 3'ss of exon 5
gtaaattatcactgagttctgatttgtttgaaatatggttgataatacactccaaagattcttaaactatatcataatctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC
|||| ||| | || | |  |   |||   |   | | |||   |||      ||   | | |||| || |||  | ||  ||| |||  ||||||| | ||| ||| || ||| | || || |||||||||||||||||||| |||||||||||
gtaagttagctctaattagtagattgcaggctgttttgtttcaaatg-----caggtagttttaagctctat-gttattgatttcagGCGTCCCTACCTGTGGTAGAGACATTCTTGGGGATCTCAAGCTCAAAGAGAGTGTTAAAGCCCACAC
















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|38478580|gb|CF962713.1|CF962713
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGT
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGT
EST: gi|33688088|gb|CF316327.1|CF316327
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCCCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|86501844|gb|CI144477.1|CI144477
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|86510934|gb|CI153567.1|CI153567
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|58675402|gb|CK064089.1|CK064089
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|33662135|gb|CF293102.1|CF293102
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|33662134|gb|CF293101.1|CF293101
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|33808808|gb|CF330289.1|CF330289
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|33680954|gb|CF309193.1|CF309193
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|218489064|gb|FG948407.1|FG948407
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|218505071|gb|FG947171.1|FG947171
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|218500313|gb|FG954965.1|FG954965
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|58693371|gb|CK082058.1|CK082058
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|38477159|gb|CF961292.1|CF961292
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|86431345|gb|CI084956.1|CI084956
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
EST: gi|218483000|gb|FG956128.1|FG956128
EST:     TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG                         ATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATGgtaaattatc ... tctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatggttgataatacactccaaagattcttaaactatatcataatctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC
    ggttgat  putative branch site (score: 5)
                             ttaaactatatcataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattatcactgagttctgatttgtttgaaatatggttgataatacactccaaagattcttaaactatatcataatctattgcagATGTCCCTATCAGTGCTAGGGATATTTTGGGAGACCTCAAGCTCAAAGAGAGTGTCAAAGCCCACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA