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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtcagtagcccaacacaagaaagaaataatggtattctgtaccaagtgattatgatctaatggcttgagttcttacacatgatcatttgatgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGA

Basic information

species Oryza sativa
transcript LOC_Os02g47600.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47600.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G046587_T02 (Zea mays), 3'ss of exon 6
agtcagtagcccaacacaagaaagaa-ataatggtattctgtaccaagtgattatgatctaatggcttgagttcttacac--------atgatcatttgatgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGA
       | |     | |  | | || |||||    |||| |   || |  || ||  | || |   ||| ||||| ||         ||  |  ||  |    |  |||| ||||||||||| ||||| ||||| || ||||||||||||||||||| ||| |||| || |||||||| |||  |||| || || |||||||||||||
------gacctttctatagaatataatataatatagttct-tgtaaactagttctgtcccaagg--ctgaattcttgcatcttatttaatcgttgttcaacatcactagGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA

upper sequence: LOC_Os02g47600.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA01G37790.1 (Glycine max), 3'ss of exon 6
agtcagtagcccaacacaagaaagaaataatggtattctgt-accaagtgattatgatctaatggcttgagttcttacacatgatcatttgatgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGA
  ||| | | |   ||  |      |||     || | ||| ||||  | |     |  |   |     | || ||       | ||  |  ||| | ||||||||||  ||||||||||||||||| |||||||||||||||||||| | |||||| | ||  |||||||| ||  | || || || || |||   || |
tttcacttgtctttcaacattgcataattcgaataatttgtcaccacttaaagtccaaatttggagaaaaattatttttttctaacaaattctgcta-cagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACTGACATCAATGAGCTTCCTCCACATCGGCTTGCTGAAA

upper sequence: LOC_Os02g47600.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA11G07530.1 (Glycine max), 3'ss of exon 6
agtcagtagcccaaca-caagaaagaaataatggtattctgtaccaagtgattatgatctaatggcttgagttcttacacatgatcatttgatgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGA
  ||| | | |   || ||    | || |      ||| |||  | | | |   |       |||    |  |  ||      | ||  |  ||| | ||||||||||  ||||||||||||||||| |||||||||||||||||||| | |||||| | ||  |||||||||||  | || || || || |||   || |
tttcacttggctttcaacattgcataattcgaataattttgtcaccacttaaagtacaaatttggagaaaaattatattttctaacaaattctgcta-cagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAA

upper sequence: LOC_Os02g47600.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 6
agtcagtagcccaacacaagaaagaaataatggtattctgtaccaagtgattatgatctaatggcttgagttcttaca-catgatcatttgatgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGA
               |||| ||      ||    |||||    | |   | | |  |    | |   ||   |    | ||   |  | |||  |   |||||||||||||| ||||||||||| || || ||||||||||| || || | ||| |||| ||| |||||||| ||  | ||||||||||| ||    || |
------------gtaacaaaaactcttaaacccaattctacctctatgtaatgtattaccttagtaagaaaccaggaatcaccttgttctgaaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTCCGTCACTACAGAGACATCAAAGAGCTTCCCCCTCACCGTCTAGCTGAAA

upper sequence: LOC_Os02g47600.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv04s0023g02050.t01 (Vitis vinifera), 3'ss of exon 5
agtcagtagcccaacacaagaaagaaataatggtattctgtaccaagtgatt-atgatctaatggcttgagttcttac-acatgatcatttgatgcaa--acagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGA
    |||  |   | |    ||  | |      | ||||  | ||  || || | ||    || |   | ||  |||| |  ||||      || |     |||||||| || |||||||| || ||||| || ||||||||||||||||| | |||||||| ||  |||||||| || || ||||| || ||||||   ||||
----agtctctatatatttaaattagacgtgttttttcttgatcatatgtttcaagacaccattgaaagtgtgattaccaggtgatacacaaatccttttgcagGGTGAAAAGGATGACAAAATAATAGCAGTGTGTGCTGATGACCCTGAGTTCCGCCACTACAAAGACATCAAAGAGATTCCCCCACATCGCCTTGCTGAGA

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|163918159|gb|EG715273.1|EG715273
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|163925750|gb|EG714586.1|EG714586
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|163926919|gb|EG715144.1|EG715144
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|58601442|gb|CK011970.1|CK011970
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|8404630|gb|AU091984.1|AU091984
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|16753343|gb|BM037722.1|BM037722
EST:     CCTATGATTTGATCAG                         GGTGAGAAAGATGACAAGATCATACCTGTTTGTGCTGATGACCCTGAATA
genomic: CCTATGA-TTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATA
EST: gi|15852955|gb|BI805751.1|BI805751
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|33823829|gb|CF337721.1|CF337721
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAG
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAG
EST: gi|58689221|gb|CK077908.1|CK077908
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|163928605|gb|EG710890.1|EG710890
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTCGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATA
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGT-GAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATA
EST: gi|58688425|gb|CK077112.1|CK077112
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|58596788|gb|CK007316.1|CK007316
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|58667772|gb|CK056458.1|CK056458
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATAC
EST: gi|58676589|gb|CK065276.1|CK065276
EST:     GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAG                         GGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGA
genomic: GATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGA

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: 66 (upstream exon), 29 (downstream exon)
Score: 99

GAACAAGTTGTCCCTGGATGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATTGATCAGgttaaatccc ... atgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgattatgatctaatggcttgagttcttacacatgatcatttgatgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGA
     ttatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtcagtagcccaacacaagaaagaaataatggtattctgtaccaagtgattatgatctaatggcttgagttcttacacatgatcatttgatgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA