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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAGATCCTTCAAATCGTATAGGTTCAAATGCTGGTGCAAATGACATCAAGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaatgtttcgagcatcaagacatttcgacaaagatagtttgtttagtgcatcactgattatctaaataactatatgtgcag

Basic information

species Oryza sativa
transcript LOC_Os04g23890.2
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.1 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G032351_T01 (Zea mays), 5'ss of exon 20
GAGAGATCCTTCAAATCGTATAGGTTCAAATGCTGGTGCAAATGACATCAAGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaatgtttcgagcatcaagacatttcgacaaagatagtttgtttagtgcatcactgattatctaaataactat--atgtgcag
||||||||| ||   |||  | ||||||| ||||| |||||| || |||||||||||| |||||||| |||| ||  | ||||||||||| |||||||||||  | || |  ||  |||| |    | | |         |    ||| || |  ||||||| || |   | |||||| |  ||||||||
GAGAGATCCCTCTTCTCGACTTGGTTCAAGTGCTGCTGCAAACGATATCAAGCAACATCCCTTTTTTGAAGATATACACTGGCCACTCATCCGTTGCATGgtgatctggaaatt--gagcctttgaagaatatcttgggtagtaattgcttggcacatcactaataaagaacataactttgcatgtgcag

upper sequence: LOC_Os04g23890.1 (Oryza sativa), 5'ss of exon 21
lower sequence: GLYMA16G19560.1 (Glycine max), 5'ss of exon 23
GAGAGATCCTTCAAATCGTATAGGTTCAAATGCTGGTGCAAATGACATCAAGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgta-----ctttgaatgtttcgagcatcaagacatttcgacaaagatagtttgtttagtgcatcactgattatctaaataactatatgtgcag----------
 ||||| ||  ||| ||||||||||||||   ||||||| ||||| |||||||||||| | ||||| |  |  ||||||||||| || || ||   |||||||     |||   || | |   | |   || ||||  || ||| || |  |       | |  |   ||||       ||  ||| || |||          
AAGAGACCCAACAAGTCGTATAGGTTCAACCACTGGTGCCAATGAAATCAAGCAACATCCTTTTTTCCGTGGAATCAATTGGCCTCTTATCCGCAACATGgtaatattcttgtgatttcttttgaagtcagtcatta-gaaaaatattgactaccgtaagtaataa-aattagtccttcaaagatacgt-cagtcattttagg

upper sequence: LOC_Os04g23890.1 (Oryza sativa), 5'ss of exon 21
lower sequence: PP1S17_314V6.1 (Physcomitrella patens), 5'ss of exon 19
GAGAGATCCTTCAAATCGTATAGGTTCAAATGCTGGTGCAAATGACATCAAGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaatgtttcga-gcatcaagaca--tttcg-------acaaagatagtttgtttagtgcatcactgattatctaaataactatatgtgcag--
                 |  | || ||   |  |||||||| |||||||||| | ||| | || |||||||||||||||||||| || |||||   |||||||  |  ||  ||   | || ||   |||  | |||       ||    ||| |||| ||        | ||  |     | |||  || ||    |  
----------------AGACTTGGGTCTCGTCGTGGTGCAAGTGACATCAAGAACCATCCATTCTTTCAAGACATCAATTGGCCTCTTATACGCAACATGgtatgtgcaagtttctaatgcttccttacagatctcgtgtcattactctcataatttgcttgaatacgaagtgcgtgcggtagtaaacatttgcttcgct

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|29685192|gb|CB681467.1|CB681467
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|86860599|gb|CI324891.1|CI324891
EST:     AGCAACATTCCTTTGTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTTAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|29618297|gb|CB623309.1|CB623309
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|29619193|gb|CB624205.1|CB624205
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|29679663|gb|CB675938.1|CB675938
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|88523276|gb|CI451086.1|CI451086
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAAGTAGATGTTCCTCTGAAACTAAGTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|86870343|gb|CI319449.1|CI319449
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCT-AACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|29680790|gb|CB677065.1|CB677065
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|29626656|gb|CB631667.1|CB631667
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|86861209|gb|CI326647.1|CI326647
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|29615866|gb|CB620878.1|CB620878
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|29685421|gb|CB681696.1|CB681696
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|25806004|gb|CA761965.1|CA761965
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|88253359|gb|CI351985.1|CI351985
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|86853887|gb|CI329333.1|CI329333
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|29612811|gb|CB617824.1|CB617824
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|29630592|gb|CB635601.1|CB635601
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|29620201|gb|CB625213.1|CB625213
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|88517987|gb|CI445540.1|CI445540
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAAGTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|29619194|gb|CB624206.1|CB624206
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|86903055|gb|CI324525.1|CI324525
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|29613428|gb|CB618441.1|CB618441
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|88531053|gb|CI459492.1|CI459492
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|86481914|gb|CI124547.1|CI124547
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|88906896|gb|CI375968.1|CI375968
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|29618974|gb|CB623986.1|CB623986
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|29646470|gb|CB651477.1|CB651477
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|38478618|gb|CF962751.1|CF962751
EST:     AGCGACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
EST: gi|38480878|gb|CF964967.1|CF964967
EST:     AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATG                         AGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA
genomic: AGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAA

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: 72 (upstream exon), 65 (downstream exon)
Score: 28

GAGAGATCCTTCAAATCGTATAGGTTCAAATGCTGGTGCAAATGACATCAAGCAACATTCCTTTTTTCAAGACATCAATTGGCCACTCATACGTTGCATGgtactttgaa ... atatgtgcagAGCCCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAACCAAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTT




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