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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcagactatttaagccagttttgttttctatgcaacctagtgtcctagttcatcttgcatcacatcttttacaaacttcggtgcactgacgagtatgatgttatttgtcaactatcgttagCTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGGACCAAAGATGGATATAATCCACTCCTTGATGATTTCAGGAACACCAAGT

Basic information

species Oryza sativa
transcript LOC_Os01g68390.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68390.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G101217_T08 (Zea mays), 3'ss of exon 12
gtaagttcagactatttaagccagttttgttttctatgcaacctagtgtcctagttcatcttgcatcacatcttttacaaacttcggtgcactgacgagtatgatgttatttgtcaactatcgttagCTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGGACCAAAGATGGATATAATCCACTCCTTGATGATTTCAGGAACACCAAGT
                                    ||   ||| | || || |  |    | |  | |||   |        | ||   |      | |    |||      ||    |     |||||||| |||| ||||||||||| ||||||||  ||||| ||||||| ||||||||||| || |||||||| || || || ||||||| |||||| ||||
-----------------------------------gtgagtcctcg-gttctcgccctctcttctccgcatgcctgcagcgtattggactaaaactaactgatgtgtcggccatcgtgcaaatccagCTTGATACTGCAGCCTTCATGGAGGAGTTTGGCATGCCGCTGAAGACGAGGACCAAAGACGGGTATAATCCGCTTCTCGACGATTTCAAGAACACAAAGT
















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|88444344|gb|CI555061.1|CI555061
EST:     AACCAGTTAAGACGAGGAGAACCATCATT                         CTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
genomic: AACCAGTTAAGACGAGGAGAACCATCATTgtaagttcag ... ctatcgttagCTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
EST: gi|88484134|gb|CI421405.1|CI421405
EST:     GACGAGGAGAACCATCATT                         CTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
genomic: GACGAGGAGAACCATCATTgtaagttcag ... ctatcgttagCTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
EST: gi|88223890|gb|CI223739.1|CI223739
EST:     AAAAGAACCCCGGTGCATTTAAACCAGTTAAGACGAGGAGAACCATCATT                         CTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
genomic: AAAAGAACCCCGGTGCATTTAAACCAGTTAAGACGAGGAGAACCATCATTgtaagttcag ... ctatcgttagCTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
EST: gi|88851279|gb|CI404331.1|CI404331
EST:     TTAAGACGAGGAGGACCATCATT                         CTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
genomic: TTAAGACGAGGAGAACCATCATTgtaagttcag ... ctatcgttagCTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
EST: gi|27578300|gb|CB000995.1|CB000995
EST:     AAAAGAACCCCGGTGCATTTAAACCAGTTAAGACGAGGAGAACCATCATT                         CTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
genomic: AAAAGAACCCCGGTGCATTTAAACCAGTTAAGACGAGGAGAACCATCATTgtaagttcag ... ctatcgttagCTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
EST: gi|88510737|gb|CI438243.1|CI438243
EST:     ACGAGGAGAACCATCATT                         CTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
genomic: ACGAGGAGAACCATCATTgtaagttcag ... ctatcgttagCTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
EST: gi|88508656|gb|CI436162.1|CI436162
EST:     AAAAGAACCCCGGTGCATTTAAACCAGTTAAGACGAGGAGAACCATCATT                         CTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
genomic: AAAAGAACCCCGGTGCATTTAAACCAGTTAAGACGAGGAGAACCATCATTgtaagttcag ... ctatcgttagCTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
EST: gi|86429111|gb|CI075792.1|CI075792
EST:     AAAAGAACCCCGGTGCATTTAAACCAGTTAAGACGAGGAGAACCATCATT                         CTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
genomic: AAAAGAACCCCGGTGCATTTAAACCAGTTAAGACGAGGAGAACCATCATTgtaagttcag ... ctatcgttagCTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
EST: gi|88323365|gb|CI553610.1|CI553610
EST:     TAAGACGAGGAGAACCATCATT                         CTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG
genomic: TAAGACGAGGAGAACCATCATTgtaagttcag ... ctatcgttagCTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttacaaacttcggtgcactgacgagtatgatgttatttgtcaactatcgttagCTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGGACCAAAGATGGATATAATCCACTCCTTGATGATTTCAGGAACACCAAGT
                 cactgac  putative branch site (score: 2)
                               atgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcagactatttaagccagttttgttttctatgcaacctagtgtcctagttcatcttgcatcacatcttttacaaacttcggtgcactgacgagtatgatgttatttgtcaactatcgttagCTTGATTCTGCTGCCTTCATGGAAGAGTTTGGACTGCCGTTGAAGACTAGGACCAAAGATGGATATAATCCACTCCTTGATGATTTCAGGAACACCAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA