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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcggagtacttttggagtttagtacttgaatgttattctatatctgaattcctaatcaagaattctattgttaacgcagctatcaattttgttatgcagGCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTTGCTAATGCTGGCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATG

Basic information

species Oryza sativa
transcript LOC_Os09g07830.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07830.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 8
--agcggagtacttttgg-agtttagtacttgaatgttattctatatctgaattcctaatcaagaattctattgttaacgcagctatcaattttgttatgcagGCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTTGCTAATGCTGGCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATG
  | | |  |  | ||   | |||||   ||| |  ||||    || | |||||  ||||  |||||  |||| |  |   |  ||||   ||  || |  ||||||||||  | ||||| || |  || |||||||||||||| |||||| |  | |||||||| || ||||| || | |||||||| |||||| |||||||
ggaacagttttatgttactattttagatattggagtttatcaactaccagaatttgtaatttagaatattattttgtaaatatgtatc---ttatttctatagGCTCCTGAGCTTTTTACAACCACTCCAGCACTTGCCATACCAAAGGCTATCACAAATGCTGGATTAGAGTCATCCCATGTTGATTTCTATGAGATTAATG

upper sequence: LOC_Os09g07830.3 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv00s0531g00050.t01 (Vitis vinifera), 3'ss of exon 9
agcggagtacttttggagtttagtacttgaatgttattctatatctgaattcctaatcaagaattctattgttaacgcagctatcaattttgttatgcagGCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTTGCTAATGCTGGCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATG
      ||||| ||| |   |   ||||  || |   | |  ||||  ||       ||       |  |  |||  ||       |||   ||  |||||| |||||||| ||||| |||| ||| || ||||| ||||| || ||| || ||||||||||| || || ||||||   |||||||||||||||| ||||
------gtactgttgaaaagtta-actt--atatcggtttcgatcttgatatgaccacagatgacttgatactaaaaca-----tgattggcttgggcagGCACCTGAATTGTTTACAACTACCCCAGCCCTTGCAATACCAAAAGCTATTTCTAATGCTGGCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATG
















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|86867692|gb|CI342669.1|CI342669
EST:     TTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA                         GCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
genomic: TTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAAgtaagccaca ... tgttatgcagGCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
EST: gi|27410210|gb|CA923280.1|CA923280
EST:     TTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA                         GCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
genomic: TTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAAgtaagccaca ... tgttatgcagGCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
EST: gi|88993566|gb|CI110387.1|CI110387
EST:     CAAAGGATTTGCAGATGCAGCTCAA                         GCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
genomic: CAAAGGATTTGCAGATGCAGCTCAAgtaagccaca ... tgttatgcagGCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
EST: gi|29640958|gb|CB645965.1|CB645965
EST:     TTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA                         GCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
genomic: TTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAAgtaagccaca ... tgttatgcagGCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
EST: gi|86498219|gb|CI140852.1|CI140852
EST:     TTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA                         GCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
genomic: TTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAAgtaagccaca ... tgttatgcagGCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
EST: gi|87020189|gb|CI259259.1|CI259259
EST:     TTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA                         GCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
genomic: TTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAAgtaagccaca ... tgttatgcagGCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
EST: gi|33683367|gb|CF311606.1|CF311606
EST:     TTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA                         GCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
genomic: TTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAAgtaagccaca ... tgttatgcagGCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
EST: gi|88906443|gb|CI375515.1|CI375515
EST:     TTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA                         GCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
genomic: TTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAAgtaagccaca ... tgttatgcagGCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
EST: gi|5607308|gb|AU075980.1|AU075980
EST:     TTGGACTGCAAGTTATTGCCCGAATCAAAGGATTTGCAGATGCAGCTCAA                         GCTCCTGAATTATTTCCCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
genomic: TTGGACTGCAAGTTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAAgtaagccaca ... tgttatgcagGCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
EST: gi|89182185|gb|CI113554.1|CI113554
EST:     TTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAA                         GCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT
genomic: TTATTGCACGAATCAAAGGATTTGCAGATGCAGCTCAAgtaagccaca ... tgttatgcagGCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattcctaatcaagaattctattgttaacgcagctatcaattttgttatgcagGCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTTGCTAATGCTGGCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATG
                        tgttaac  putative branch site (score: 2)
                                          ttttgtt  putative PPT
                                    tatcaattttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcggagtacttttggagtttagtacttgaatgttattctatatctgaattcctaatcaagaattctattgttaacgcagctatcaattttgttatgcagGCTCCTGAATTATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTTGCTAATGCTGGCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG