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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgttaaagttttcctggtggagaatatcaactggaatggaagttacgctagttatttgttaatggaaaccatgaatcttgccttttcattggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTGTTCTCTCTGGTGCAAACATAATGTGTCCTGGATTGACATCTCCAGGTGG

Basic information

species Oryza sativa
transcript LOC_Os01g21180.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g21180.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G180990_T02 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------------------------aattgttaaagttttcctggtggaga-atatcaactggaatggaagttacgctag---ttatttgttaatggaaacca-------tgaatcttgccttttcattggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTGTTCTCTCTGGTGCAAACATAATGTGTCCTGGATTGACATCTCCAGGTGG
                                                                             |    | |   |||| | | | |  | | ||| | | |    |       | ||    | |||||||   | | |  |       ||||   ||   || |||| ||||||||||||| |||||||| |||||||||||||||||||| |||||||| |||||||| ||||| |||||||||||||||||||| ||||| || || |||||
gtaatttcttccttccaaattttctatctatgcaccctatttttcaagatgtatagcatgatgtgcgaaacaaatttagggatcatcctttttcagtttgtcatacatctattcgggctgtgtcattgttaaaattgatttgttggagcatattaactagtatgaaaactgtgcttgcatttgatcagATCCTGATATCATGAAAAAGTTCCAAGTGGATAGAGGTGCTATCAAATTTGTTCTATCTGGCGCAAACATAATGTGTCCTGGGTTGACTTCACCTGGTGG

upper sequence: LOC_Os01g21180.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G09150.1 (Arabidopsis thaliana), 3'ss of exon 5
aattgttaaagttttcctggtggagaatatcaactggaatggaagttacgctagttatttgttaatg--gaaaccatgaatcttgccttttcattggat--cagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTGTTCTCTCTGGTGCAAACATAATGTGTCCTGGATTGACATCTCCAGGTGG
 | | ||| |   | | ||   || |     ||    | | | ||||     | |||      ||||   |||   ||     ||  | ||    |  |  |||| ||  | || ||||||| ||| ||||| |||||||| || || ||||||||||| ||||||||||||||||||||||||||  | ||||| || || ||
-acttttaca---tacttgaatgatacatagaaagaaacttggagttttttcaattagccacgaatgtcaaaaatttggcagctgaatgtttggagttttgcagACCCAAATATAATGAAGAGGTTTCAAGTTGATAGAGGTGCCATAAAGTTTGTTCTGTCTGGTGCAAACATAATGTGTCCTGGTCTTACATCCCCGGGAGG
















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|88361922|gb|CI682096.1|CI682096
EST:     AATATCCGTGATGGTCCTTACATGCCAACCTTGCCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: AATATCCGTGATGGTCCTTACATGCCAACCTTGC-GCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88664198|gb|CI673276.1|CI673276
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAG
EST: gi|88831835|gb|CI369517.1|CI369517
EST:     GTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTT
genomic: GTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|163921070|gb|EG710133.1|EG710133
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTT
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTT
EST: gi|88326211|gb|CI660024.1|CI660024
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAA
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAA
EST: gi|88727487|gb|CI751142.1|CI751142
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|33688443|gb|CF316682.1|CF316682
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGATGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88692766|gb|CI736341.1|CI736341
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTT
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTT
EST: gi|29289887|gb|CB483501.1|CB483501
EST:     AATATCCGTGATGGTCCTTACATGCCAACCCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: AATATCCGTGATGGTCCTTACATGCCAA-CCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88584551|gb|CI702113.1|CI702113
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTG
EST: gi|33812764|gb|CF332270.1|CF332270
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|29687412|gb|CB683687.1|CB683687
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88732421|gb|CI755598.1|CI755598
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGT-CCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88581529|gb|CI698523.1|CI698523
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88582517|gb|CI699934.1|CI699934
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88573361|gb|CI664932.1|CI664932
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCG
EST: gi|88329462|gb|CI648521.1|CI648521
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGA
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGA
EST: gi|218488231|gb|FG951457.1|FG951457
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88347712|gb|CI655065.1|CI655065
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88388325|gb|CI627864.1|CI627864
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|86522655|gb|CI162861.1|CI162861
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88726864|gb|CI750519.1|CI750519
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCCTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|163928391|gb|EG714711.1|EG714711
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|55412623|gb|CV724999.1|CV724999
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88726544|gb|CI750199.1|CI750199
EST:     AATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCCTTCTTCATCACT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: AATATCCGTGATGGTCCTTACATGCCAACCTTGCGCC-TTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88376867|gb|CI639192.1|CI639192
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGC
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGC
EST: gi|87012993|gb|CI297220.1|CI297220
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88405694|gb|CI609593.1|CI609593
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|33665495|gb|CF296462.1|CF296462
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88359324|gb|CI679851.1|CI679851
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88306080|gb|CI635086.1|CI635086
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88421818|gb|CI611697.1|CI611697
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|66917257|gb|CX104105.1|CX104105
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
EST: gi|88324957|gb|CI644968.1|CI644968
EST:     CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT                         ATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG
genomic: CAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttct ... attggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacgctagttatttgttaatggaaaccatgaatcttgccttttcattggatcagATCCTGACATCATGAAGAAGTTCCAAGTGGATAGAGGCGCTATCAAGTTTGTTCTCTCTGGTGCAAACATAATGTGTCCTGGATTGACATCTCCAGGTGG
              tgttaat  putative branch site (score: 3)
                                 tcttgccttttcatt  putative PPT
      tagttatttgttaat  TA-rich tract