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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaggcacgaaacctttatcatctctgagttcctaagcattgcctgaaagaaaaccaatgactatatgcttacatcttgattctgtctatttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCAATCGCTATGCTGGTTTCGATGGGCTTTGATGGAAATGCTGCAAGACAGG

Basic information

species Oryza sativa
transcript LOC_Os01g16330.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16330.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G157316_T02 (Zea mays), 3'ss of exon 1
---acaaggcacgaaacctttatcatctctgagttcctaagcattgcctgaaagaaaaccaatgactatat-gcttacatcttgattctgtctatttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCAATCGCTATGCTGGTTTCGATGGGCTTTGATGGAAATGCTGCAAGACAGG
   |  | | || ||   |||  |||||        | ||  | |  |||      |  | || |   | | ||  || |  ||| | |||    | ||   ||||  | |   || ||||||| || ||| |||||||||| ||||| || ||  | ||||||||||| || |||||||||||||| |||   ||||| ||||
gggagtacgtactaagaattt--catctaatgaaagcaaattactagctgttgtttagtcgatcagcctgttgcgcac-tgctgactttgttctctcaa-gcagAATCAGCCATCAACTGGATTTGCACCTATCGTGGAGCCTCCAGAGTCCTCCGTTGCTATGCTGGTCTCAATGGGCTTTGATGGCAATAACGCAAGGCAGG
















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|58604468|gb|CK014996.1|CK014996
EST:     CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAG                         AACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
genomic: CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAGgttagttttt ... tttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
EST: gi|29661709|gb|CB657984.1|CB657984
EST:     CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAG                         AACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
genomic: CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAGgttagttttt ... tttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
EST: gi|89198484|gb|CI007544.1|CI007544
EST:     AACATGAGTTCTCGTACAAGCCGTGCTGTGCAG                         AACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
genomic: AACATGAGTTCTCGTACAAGCCGTGCTGTGCAGgttagttttt ... tttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
EST: gi|88398176|gb|CI588064.1|CI588064
EST:     CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAG                         AACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
genomic: CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAGgttagttttt ... tttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
EST: gi|29661710|gb|CB657985.1|CB657985
EST:     CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAG                         AACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
genomic: CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAGgttagttttt ... tttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
EST: gi|218487612|gb|FG952665.1|FG952665
EST:     CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAG                         AACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
genomic: CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAGgttagttttt ... tttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
EST: gi|22306429|gb|BQ907651.1|BQ907651
EST:     TCGGAAACATGAGTTCTCGTACAACCCGGTGCTGTGCAG                         AACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCG
genomic: TCGGAAACATGAGTTCTCGTACAAGCC-GTGCTGTGCAGgttagttttt ... tttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
EST: gi|89184669|gb|CI007094.1|CI007094
EST:     CCGTGCTGTGCAG                         AACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
genomic: CCGTGCTGTGCAGgttagttttt ... tttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
EST: gi|33689953|gb|CF318192.1|CF318192
EST:     CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAG                         AACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCACAATCTTCA
genomic: CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAGgttagttttt ... tttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
EST: gi|23513675|gb|BU673250.1|BU673250
EST:     CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAG                         AACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
genomic: CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAGgttagttttt ... tttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
EST: gi|89193040|gb|CI050338.1|CI050338
EST:     CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAG                         AACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
genomic: CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAGgttagttttt ... tttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
EST: gi|29657193|gb|CB653468.1|CB653468
EST:     CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAG                         AACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
genomic: CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAGgttagttttt ... tttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
EST: gi|86427044|gb|CI072141.1|CI072141
EST:     CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAG                         AACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA
genomic: CCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAGgttagttttt ... tttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 70 (upstream exon), 63 (downstream exon)
Score: 3

ATTTTTCGCAAGAATTTTCGCACCTTCTTCGGGAGGTTCATCTAGGCCCTCCAGGAGTCTGGTCGGAAACATGAGTTCTCGTACAAGCCGTGCTGTGCAGgttagttttt ... tttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCAATCGCTATGCTGGTTTCGATGGGCTTTGATGGAAATGCTGCAAGACAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaagaaaaccaatgactatatgcttacatcttgattctgtctatttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCAATCGCTATGCTGGTTTCGATGGGCTTTGATGGAAATGCTGCAAGACAGG
                                         tctattt  CT-rich tract
                                       tgtctatttaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaggcacgaaacctttatcatctctgagttcctaagcattgcctgaaagaaaaccaatgactatatgcttacatcttgattctgtctatttaatatagAACAATCAGCCATCTGGATTCGCTCCTGTCGTGGAGCCCCCAGAATCTTCAATCGCTATGCTGGTTTCGATGGGCTTTGATGGAAATGCTGCAAGACAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - cacgaaa
- - - - - - - - - - - - - - - - - - - - ttgcctg
- - - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttac