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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttcttctcatacataaatcttcatacaagatgagctaactcgttaacggcgctgcaagcctctacaaatcttacaaataaatcgaatggctttaattactccttttccaattcttcaaacag

Basic information

species Oryza sativa
transcript LOC_Os01g09300.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g09300.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G147882_T02 (Zea mays), 5'ss of exon 9
GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttcttctcatacataaatcttca--tacaagatgagctaactcgttaacggcgctgcaagcctctacaaatcttaca--aataaatcgaatggctttaattactccttttccaattcttcaaacag
|||||||||||||||||||||| ||||||| ||||||||  | || ||||||||| |  | | | |  ||||| |  |   | |    || |    |  |     |||       ||  || |||      || ||  ||||  ||                                
GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcgtaacgtccgttcatcttgagttggtaaactgccttagctatgcatattactgttgtaacctgaaagtctcttggcaagaagacgaaaagc--------------------------------
















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|25803965|gb|CA759926.1|CA759926
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|29662625|gb|CB658900.1|CB658900
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|22307986|gb|BQ909208.1|BQ909208
EST:     AGATGGACGAGAACGTCATTCT                         ATTGCGTTCTGTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCC
genomic: AGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCT-TTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCC
EST: gi|218497246|gb|FG965662.1|FG965662
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCATGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|33690519|gb|CF318758.1|CF318758
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCCACGATTGCGTAGTCGAGTGCCTGCC
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAG-CCACGATTGCGTAGTCGAGTGCCTGCC
EST: gi|29615163|gb|CB620176.1|CB620176
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|33655635|gb|CF278249.1|CF278249
EST:     TGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: TGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|29615162|gb|CB620175.1|CB620175
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|33658108|gb|CF280722.1|CF280722
EST:     GATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|29678794|gb|CB675069.1|CB675069
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|29638841|gb|CB643850.1|CB643850
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|33683276|gb|CF311515.1|CF311515
EST:     GTCAACCCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCCACGATTGCGTAGTCGAGTGCCTGCC
genomic: GTCAA-CCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAG-CCACGATTGCGTAGTCGAGTGCCTGCC
EST: gi|218500447|gb|FG953831.1|FG953831
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACG
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACG
EST: gi|33690409|gb|CF318648.1|CF318648
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|112785412|gb|EE590632.1|EE590632
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|29665424|gb|CB661699.1|CB661699
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|29680385|gb|CB676660.1|CB676660
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|218481515|gb|FG954235.1|FG954235
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|33677763|gb|CF306002.1|CF306002
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|218492870|gb|FG955679.1|FG955679
EST:     GTCAACCTTACATCGCA-TGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGCACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCG-AGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|29642174|gb|CB647181.1|CB647181
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
EST: gi|38471976|gb|CF956107.1|CF956107
EST:     GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCT                         ATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA
genomic: GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttct ... cttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAACCTTACATCGAGTGGTCTTAGATGGACGAGAACGTCATTCTgtaagtttcttctcatacataaatcttcatacaagatgagctaactcgttaacggcgctgcaagcctctacaaatcttacaaataaatcgaatggctttaattactccttttccaattcttcaaacag

- - - - - - - - - - - -  GATGGA