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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACAAAAAGTGGAAGGAGGGGTTCTATGTCACTGCCTTGGCCACAGCAGGAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGgtacgtttggagtgtccaagagccttgtaaaattgaattcattttagcagcaagctacactgactatcaattgaatatgtaaaagtcttgagattttattatctcgcatatctcttttgtaggtag

Basic information

species Oryza sativa
transcript LOC_Os01g10150.2
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10150.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G045259_T02 (Zea mays), 5'ss of exon 14
AAACAAAAAGTGGAAGGAGGGGTTCTATGTCACTGCCTTGGCCACAGCAGGAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGgtacgt---ttggagtgtccaagagcctt-gtaaaattgaattcattttagcagcaagctacactgactatcaattgaat---atgtaaaagt-cttgagattttattatctcgcatatctcttttgtaggtag----------------------------------------------
||||||||||||||||||||| ||||||||||||||  |||| ||||| |||||||||||||| || || |||||||| || |||||||||||   |||||||  |   ||   ||| ||  |  | |  ||       |  | |   | | |  ||      | |   |||   ||||    || | ||||   || ||||  |||      ||  ||      |      ||                                              
AAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGCAACAGCTGGAAGCCGATGGGCAGTTGTCATGTCCCGCAATGCTGGTTTCACTTCTCAGgtatatgtgttactgtgcccttggtcttaagtgtccacaaccttacagtggaatgaaatagatcggtagatctgctgaaattaatctgaaagaatttaagatcgtatggatatgcgaattgagaatcacaaaagttccattactgaaacactataccgaacgcaccaatttattttgtag

upper sequence: LOC_Os01g10150.2 (Oryza sativa), 5'ss of exon 14
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 14
AAACAAAAAGTGGAAGGAGGGGTTCTATGTCACTGCCTTGGCCACAGCAGGAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGgta-----cgtttggagtgtccaagagccttgtaaaattgaattcattttagcagc---aagctacactgactatcaattgaatatgtaaaagtcttga--gattt-----tattatc-tcgcatatctcttttgtaggtag---------------------------------
 || || || |||   || || ||||| || ||  |  |||||||||| ||||||||||||| ||| |||||||| || ||||| |||||| |  ||||||||     || |   ||  | |  ||     | |||    |    ||||| ||  |    |     |     ||| || | |||    | |  |  |||   ||||     |  | || ||| | ||| | |   ||  |                                   
CAATAAGAAATGGCGAGAAGGCTTCTACGTTACATCTATGGCCACAGCGGGAAGCCGATGGGGTGTAGTTATGTCGCGAAACGCAGGTTTCTCTGATCAGgtaattagcgctctaagcctacttgatttacgaaaaccgcatactatttttgcttcttcgactcggagcagatatgaagtaaatgaaaatatttgctgaccaatttagaattcctgtcatcggacatcacctgattacattcctctctcttaccgaatgtatttgccctctgcag
















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|29688779|gb|CB685054.1|CB685054
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAG                         G
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGgtacgtttgg ... ttgtaggtag-
EST: gi|29688779|gb|CB685054.1|CB685054
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAG                         G
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGgtacgtttgg ... ttgtaggtag-
EST: gi|89179002|gb|CI043507.1|CI043507
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|88263532|gb|CI367306.1|CI367306
EST:     GAAGCCGATGGGCTGTGGTTATGTCCC-GAACGCT-GTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|89192726|gb|CI050024.1|CI050024
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|88513442|gb|CI440948.1|CI440948
EST:     AGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: AGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|89184391|gb|CI046956.1|CI046956
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|29670786|gb|CB667061.1|CB667061
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|87024232|gb|CI256973.1|CI256973
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|29645032|gb|CB650039.1|CB650039
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAG                         G
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGgtacgtttgg ... ttgtaggtag-
EST: gi|29645032|gb|CB650039.1|CB650039
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAG                         G
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGgtacgtttgg ... ttgtaggtag-
EST: gi|29626995|gb|CB632006.1|CB632006
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|88514991|gb|CI442645.1|CI442645
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|86483807|gb|CI126440.1|CI126440
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|86526996|gb|CI167202.1|CI167202
EST:     GATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|88275485|gb|CI395336.1|CI395336
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACCCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|86864077|gb|CI332966.1|CI332966
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAG                         TAGAACTTGATTTCTTATATCCGAGTGAAGGAATCCATCAACGCTGGGATA
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGgtacgtttgg ... ttgtaggtagTAGAACTTGATTTCTTATATCCGAGTGAAGGAATCCATCAACGCTGGGATA
EST: gi|89193060|gb|CI050358.1|CI050358
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|396941388|gb|HO188597.1|HO188597
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|89195193|gb|CI051306.1|CI051306
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|88271617|gb|CI387670.1|CI387670
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|88484372|gb|CI421643.1|CI421643
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|58611769|gb|CK039481.1|CK039481
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|29632066|gb|CB637075.1|CB637075
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|88849770|gb|CI001476.1|CI001476
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|86600035|gb|CI258375.1|CI258375
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|86483022|gb|CI125655.1|CI125655
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|88294949|gb|CI522903.1|CI522903
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGG                         TAGTANAACTTGATTTCTTATATCCGAGTGAAGGAATCCATCAACGCTGG
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCA-Ggtacgtttgg ... ttgtaggtagTAG---AACTTGATTTCTTATATCCGAGTGAAGGAATCCATCAACGCTGG
EST: gi|89166036|gb|CI103126.1|CI103126
EST:     TATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: TATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|89180610|gb|CI044889.1|CI044889
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|87040610|gb|CI195232.1|CI195232
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAG                         G
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGgtacgtttgg ... ttgtaggtag-
EST: gi|87040610|gb|CI195232.1|CI195232
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAG                         G
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGgtacgtttgg ... ttgtaggtag-
EST: gi|89180204|gb|CI044483.1|CI044483
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|3766584|gb|AU030694.1|AU030694
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAG                         G
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGgtacgtttgg ... ttgtaggtag-
EST: gi|3766584|gb|AU030694.1|AU030694
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAG                         G
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGgtacgtttgg ... ttgtaggtag-
EST: gi|27546382|gb|CA764550.2|CA764550
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|88291104|gb|CI527494.1|CI527494
EST:     GAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg
EST: gi|87024182|gb|CI256923.1|CI256923
EST:     GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGGTAG                      
genomic: GAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATC----AGgtacgtttgg ... ttgtagg

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: 74 (upstream exon), 74 (downstream exon)
Score: 69

AAACAAAAAGTGGAAGGAGGGGTTCTATGTCACTGCCTTGGCCACAGCAGGAAGCCGATGGGCTGTGGTTATGTCCCGGAACGCTGGTTTCACACATCAGgtacgtttgg ... ttgtaggtagTAGAACTTGATTTCTTATATCCGAGTGAAGGAATCCATCAACGCTGGGATAGTGGTTATCGCATAACTGCAACAGCAGCCACATGTGACCAGGTGGCTTT




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