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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggaaacataaaagctggaatagtttttaatagttctcccattctgttcatttcttatgattagtgattgagctactgaatgccattgtctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCATTTCTGGTTGGACGTGGAGCACATCCAGGAGGCAATCCAGAATGTCTTGG

Basic information

species Oryza sativa
transcript LOC_Os07g32230.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g32230.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G025242_T02 (Zea mays), 3'ss of exon 4
---tgggaaacataaaagctggaatagtttttaatagttctcc-cattctgttcatttcttatgatta-gtgattgagctactgaatgccattgtctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCATTTCTGGTTGGACGTGGAGCACATCCAGGAGGCAATCCAGAATGTCTTGG
    | || |  ||   ||  |  | | ||  |  |   ||   |  || | |  ||| ||| | | |   ||   | | |||     ||||| || ||  ||||||||||||  | || |||||| |    | |||  | ||  | ||||||||||||||| ||||||||||||||||||||||||| |||||||| ||| |||
aatggagagagctatttgcctgttttgattgaagaaccacttggccctccgatttttttttacgctaacaggacacacccact---ccccattatcgtt--gcagGGTTTTGCGCTCGATGTTTTAACCCAAGCAGGCGTGATCAAATCCCACCATTTCTGGCTGGACGTGGAGCACATCCAGGAGGCGATCCAGAACGTCCTGG

upper sequence: LOC_Os07g32230.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0404g00020.t01 (Vitis vinifera), 3'ss of exon 4
tgggaaacataaaagctggaatagtt--tttaatagttctcccat-tctgttcatttcttatgattagtgattgagctactgaatgccattgt---ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCATTTCTGGTTGGACGTGGAGCACATCCAGGAGGCAATCCAGAATGTCTTGG
         |    ||| |||   ||  || ||  ||| |   |  | ||   ||| |||   || | | | |     || ||  |||||| |   |    |||||||  | |   | ||| || ||| |||  | ||  ||||||  || |||||||||||||| || ||||||||||| || || || || |||||||||||||
----tttttttcctgctagaagttttccttcaaaggttttttgaaatttgaatattgcttg-aataaattacttgctcacagag-gccatttttaaccacatgcagGGCATAGTGCTCGAGATTCTAGTTGCACTGGGCGTCATTCGATCACACCATTTCTGGTTAGATGTGGAGCACATTCAAGAAGCTATTCAGAATGTCTTGG
















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|88987063|gb|CI034104.1|CI034104
EST:     TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAG                         GGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
genomic: TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAGgtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
EST: gi|22304929|gb|BQ906151.1|BQ906151
EST:     TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAG                         GGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
genomic: TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAGgtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
EST: gi|55408517|gb|CV720893.1|CV720893
EST:     TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAG                         GGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
genomic: TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAGgtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
EST: gi|89168633|gb|CI038485.1|CI038485
EST:     TTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAG                         GTTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
genomic: TTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAGgtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
EST: gi|86413511|gb|CI019096.1|CI019096
EST:     TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAG                         GGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
genomic: TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAGgtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
EST: gi|89192023|gb|CI393380.1|CI393380
EST:     CTTTCTGGCAGG                         GGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCA
genomic: CTTTCTGGCA-Ggtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCA
EST: gi|89196563|gb|CI400733.1|CI400733
EST:     TTGCCAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAG                         GGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
genomic: TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAGgtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
EST: gi|87038307|gb|CI192929.1|CI192929
EST:     TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAG                         GGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
genomic: TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAGgtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
EST: gi|89182717|gb|CI114086.1|CI114086
EST:     GATTGTCTTCTTCTCTTTCTGGCAG                         GGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
genomic: GATTGTCTTCTTCTCTTTCTGGCAGgtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
EST: gi|86841734|gb|CI337412.1|CI337412
EST:     CTTCTTCTCTTTCTGCCAG                         GGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
genomic: CTTCTTCTCTTTCTGGCAGgtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
EST: gi|38480495|gb|CF964584.1|CF964584
EST:     CTTCTTCTCTTTCTGCCAG                         GGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
genomic: CTTCTTCTCTTTCTGGCAGgtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
EST: gi|33680755|gb|CF308994.1|CF308994
EST:     TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAG                         GGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
genomic: TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAGgtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
EST: gi|86536155|gb|CI176361.1|CI176361
EST:     TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAG                         GGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
genomic: TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAGgtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
EST: gi|89173551|gb|CI041444.1|CI041444
EST:     TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAG                         GGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
genomic: TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAGgtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
EST: gi|33682369|gb|CF310608.1|CF310608
EST:     TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAG                         GGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
genomic: TTGCAAAATTCTTATGCATCAAAGGGATTGTCTTCTTCTCTTTCTGGCAGgtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
EST: gi|88262975|gb|CI366749.1|CI366749
EST:     CTTTCTGGCAG                         GGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT
genomic: CTTTCTGGCAGgtaatcatct ... ctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcatttcttatgattagtgattgagctactgaatgccattgtctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCATTTCTGGTTGGACGTGGAGCACATCCAGGAGGCAATCCAGAATGTCTTGG
                                         ttgtcttttt  CT-rich tract
     atttcttatgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgggaaacataaaagctggaatagtttttaatagttctcccattctgttcatttcttatgattagtgattgagctactgaatgccattgtctttttgcagGGTTTTGCATTAGAGGTTTTAGCTGCCGTAGGGATCATTCAGTCCCACCATTTCTGGTTGGACGTGGAGCACATCCAGGAGGCAATCCAGAATGTCTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - acataaa
- - - - - - -agctgga
- - - - - - - - - - - - - - - - - ttctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgc