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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTGGTATTGAAGACACTTTGGTGGCTGACCTGAATTTTATCTATGTTGTTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTGgtgagttatcgcctaatgagtctttcactggacaggatttttttcattcattgaacaatcactggtcctggtggttctcggagcgcaggaaaccaaaatt...

Basic information

species Oryza sativa
transcript LOC_Os07g12530.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g12530.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G031780_T02 (Zea mays), 5'ss of exon 4
GCCTGGTATTGAAGACACTTTGGTGGCTGACCTGAATTTTATCTATGTTGTTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTGgtgagttatcgcctaatga-gtctttcactggacaggatttttttcattcattgaacaatcactggtcctggtggttctcggagcgcaggaaaccaaaatt--
||||||||||||||| |||||||| ||||| ||||||||||||||||||||||||||| |||| || ||  | |||||||||||||| |||||||||||||| | |   | | |||||| |   ||||   |  |      |  |||    ||  |    ||    |  |  |  |  |   | |   ||    |    |   
GCCTGGTATTGAAGATACTTTGGTTGCTGATCTGAATTTTATCTATGTTGTTGCACGTGTTTTAGAGTTCTTGAACCCTGAACTACAAAGGACATCACTGgtaaatgcactcttaatgatgaagttcatgtgcaaatgagatactcaactgtttcatg-ccatgcatttt--ttttctttaaaacatgggttttccctttaat
















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|29615296|gb|CB620308.1|CB620308
EST:     TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTG                         GTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC
genomic: TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTGgtgagttatc ... tatattatagGTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC
EST: gi|29677141|gb|CB673416.1|CB673416
EST:     TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTG                         GTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC
genomic: TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTGgtgagttatc ... tatattatagGTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC
EST: gi|29615293|gb|CB620305.1|CB620305
EST:     TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTG                         GTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC
genomic: TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTGgtgagttatc ... tatattatagGTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC
EST: gi|29615266|gb|CB620278.1|CB620278
EST:     TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTG                         GTAGGAATTGTCAAGGATATAAAGGAATCTATGCT
genomic: TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTGgtgagttatc ... tatattatagGTAGGAATTGTCAAGGATATAAAGGAATCTATGCT
EST: gi|29619070|gb|CB624082.1|CB624082
EST:     TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTG                         GTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC
genomic: TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTGgtgagttatc ... tatattatagGTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC
EST: gi|29615258|gb|CB620270.1|CB620270
EST:     CTGCACGTATTTTGGAATGTCTAAACCCTGAACTACAGAGGACATCACTG                         GTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC
genomic: TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTGgtgagttatc ... tatattatagGTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC
EST: gi|29615291|gb|CB620303.1|CB620303
EST:     TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTG                         GTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAG
genomic: TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTGgtgagttatc ... tatattatagGTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAG
EST: gi|29615505|gb|CB620517.1|CB620517
EST:     TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTG                         GTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC
genomic: TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTGgtgagttatc ... tatattatagGTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC
EST: gi|29615222|gb|CB620235.1|CB620235
EST:     TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTG                         GTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC
genomic: TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTGgtgagttatc ... tatattatagGTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC
EST: gi|29615327|gb|CB620339.1|CB620339
EST:     TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTG                         GTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC
genomic: TTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTGgtgagttatc ... tatattatagGTAGGAATTGTCAAGGATATAAAGGAATCTATGCTTGAAGAAGTTGATTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTGGTATTGAAGACACTTTGGTGGCTGACCTGAATTTTATCTATGTTGTTGCACGTATTTTGGAATTTCTAAACCCTGAACTACAGAGGACATCACTGgtgagttatcgcctaatgagtctttcactggacaggatttttttcattcattgaacaatcactggtcctggtggttctcggagcgcaggaaaccaaaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA