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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttcagttactctcgttttctaggtgcttgtaatctgattttatcccatcttgctgaagcaacttttcgtactccag

Basic information

species Oryza sativa
transcript LOC_Os06g45840.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45840.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G057408_T03 (Zea mays), 5'ss of exon 2
CTGAGCTTGCTGTCATCATGTAATTCTGGTGG---GGACCCAATTAAGTCTGAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttcagttactctc-gttttc-taggtgcttgtaatctgattttatcccatcttgctgaagcaacttttcgtactccag
  ||| ||||| ||||||| ||  | ||||||   |||||   | || ||||||| ||||||||||||||||||||| |||||| ||||||| || | | |||||  |||| || ||||||  | ||| || ||| |  | | |||||    | ||||||||   || | | ||| |     ||||
-GGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCTGAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCTgtaaaccttctgtcactctccatgttcatatgtggtcatgacctgatgcgctgccatcttgactaacccaatttgcaattgccag

upper sequence: LOC_Os06g45840.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G170148_T01 (Zea mays), 5'ss of exon 8
CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttcagttactctcgttttctaggtgcttgtaatctgattttatcccatcttgctgaagcaacttttcgtactccag
                      ||  |||||||||||   ||||  |||||||||||||||||| ||||||||| |||||| ||||||| || ||| |||||  |||| |  |||| |  ||  |  ||| || | | |||||    | ||||||||   || | | ||| |     ||||
--------------------CTATGGTGGTGGGGACCATGTTAAACCTGAAGGCATGGAAAATCATGGATCTCCTCAGAGTGGCCATCTTCCATTCCTgtaaaccttctgccactccctgttcatttgtggttatgacctgatgcactgccatcttgactaacccaatttgcaattgccag
















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|218486576|gb|FG956240.1|FG956240
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|218500576|gb|FG960552.1|FG960552
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|86505486|gb|CI148119.1|CI148119
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|218481447|gb|FG951027.1|FG951027
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTG
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTG
EST: gi|88216733|gb|CI216582.1|CI216582
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|38474825|gb|CF958958.1|CF958958
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|86539300|gb|CI179506.1|CI179506
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|27545921|gb|CA764047.2|CA764047
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|88253726|gb|CI352352.1|CI352352
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCACTT
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|86491190|gb|CI133823.1|CI133823
EST:     GATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: GATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|86828394|gb|CI276939.1|CI276939
EST:     CCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: CCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|89189650|gb|CI049189.1|CI049189
EST:     AAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: AAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|218489538|gb|FG952484.1|FG952484
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|29637643|gb|CB642652.1|CB642652
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|88473994|gb|CI411265.1|CI411265
EST:     CCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: CCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|86430932|gb|CI083355.1|CI083355
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|218494859|gb|FG953214.1|FG953214
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGATGGAGAACTGCTTGTATGCGGACGAAGCTTC
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTC
EST: gi|89177323|gb|CI250772.1|CI250772
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|88842228|gb|CI081484.1|CI081484
EST:     ATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: ATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|218495544|gb|FG956087.1|FG956087
EST:     TCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: TCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|58677571|gb|CK066258.1|CK066258
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|88224111|gb|CI223960.1|CI223960
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
EST: gi|27334389|gb|CA882840.1|CA882840
EST:     GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCAT                         GGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT
genomic: GAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttc ... cgtactccagGGTAACAAGTGAGTGAGGGAGAACTGCTTGTATGCGGACGAAGCTTCAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAGCTTGCTGTCATCATGTAATTCTGGTGGGGACCCAATTAAGTCTGAAGGCATGGAAAATCTTGGATCTCCACAGAGTTGCCATCTCCCGTTCATgtaatacttcagttactctcgttttctaggtgcttgtaatctgattttatcccatcttgctgaagcaacttttcgtactccag

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