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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaagatatcttgaaggttttattaatttggcttatccagtttcatggttccgtggtgcttgctgtctgattatcgtgcaaacaagaatgttggg...

Basic information

species Oryza sativa
transcript LOC_Os07g01930.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g01930.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM5G856338_T01 (Zea mays), 5'ss of exon 3
GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaagatatcttgaaggttttattaatttggcttatccagtttcatggttccgtggtgcttgctgtctgattatcgtgcaaacaagaatgttggg----
|||||||| || ||||| ||  ||||||||||| ||||||||||||||||||||||||||||||||||||| || ||||| |||||||| ||||    | |||      | ||| ||| ||| ||   ||   | ||  |  |   |||||| ||||  ||||    ||||||  || |        
GATGTAAACTACTATAACAAATTAGAAGATCCAGCAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGGCTCACAGAGACgtaagtcaagacccttcgaaca---gagtaacttg-cttctcttattattttgtctccagaatcttgctatctgtgtatcacagaaacaaacatttcaatattt

upper sequence: LOC_Os07g01930.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G013607_T06 (Zea mays), 5'ss of exon 2
GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaagatatcttgaaggttttattaatttggcttatccagtttcatggttccgtggtgcttgctgtctgattatcgtgcaaacaagaatgttggg-----
|||||||| |||||||| ||| ||||||||||| ||||||||||||| ||||||||||||||||||||||| || |||||||||||||| |||||   |||||      | ||| |    |||| | || || ||  |   || |   | |||| | |         | |    ||| ||| |     
GATGTAAAATATTATAACAAGTTAGAAGATCCAGCAGATGAAGAAAACGATATGCTTGACCTTGCATTTGGGCTCACAGAAACgtaagtcaagatcctttgaaca---gagtaactcttattatactgtctcctgaattt-tgctatct-ctgtataacggagacagacatttcaattttgagtattt

upper sequence: LOC_Os07g01930.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT4G05450.1 (Arabidopsis thaliana), 5'ss of exon 7
GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaagatatcttgaaggttttattaatttggcttatccagtttcatggtt--ccgtggtgcttgctgtctgattatcgtgcaaacaagaatgttggg
|||    | || ||||| || || ||||| |||||||||||||| |||||||||||||| ||||| ||||| || ||||||||||||       | ||||     |      ||        |   ||| | || |||  |  |  ||      || | ||       |  ||||   | |  | 
GATACTGAATACTATAACAAACTTGAAGAACCAACAGATGAAGAGAATGATATGCTTGATCTTGCTTTTGGGCTCACAGAAACgtaaa--gtcctctcttactcttaaagcaaacacaaaacaagaagtctaattgtttactttaatgagaaa-gtatcatatgttcccggacaaatgtttcag-

upper sequence: LOC_Os07g01930.1 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ35997 (Selaginella moellendorffii), 5'ss of exon 3
GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaagatatcttgaaggttttattaatttggcttatcca--gtttcatggttccgtggtgcttgctgtctgattatcgtgcaaacaagaatgttggg
||||  || | ||||   | |||  | || ||| | || || || ||||| |||||||| |||||||||||||||||||| |||||||  |   ||   |   ||||  | |  |||  | ||   |  ||||  | ||| | || |  ||| | | | |                         
GATGAGAAGTTTTATCGGATGCTCAAGGAGCCATCGGACGAGGAGAATGACATGCTTGATCTTGCATTTGGACTTACAGAGACgtaagctatt-tactgttgtggttgaactcttttttcgtactaattgttttcttgtttcctgtt-tttgttttttcag------------------------

upper sequence: LOC_Os07g01930.1 (Oryza sativa), 5'ss of exon 7
lower sequence: EFJ36222 (Selaginella moellendorffii), 5'ss of exon 4
GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaagatatcttgaaggttttattaatttggcttatccagtttcatggttccgtggtgcttgctgtctgattatcgtgcaaacaagaatgttggg
||||  || | ||||   | |||  | || ||| | || || || || || |||||||| |||||||||||||||||||| |||||||  |   ||   |   ||||     || |     ||     |||| || ||||   ||  ||| | | | |                         
GATGAGAAGTTTTATCGGATGCTCAAGGAGCCATCGGACGAGGAGAACGACATGCTTGATCTTGCATTTGGACTTACAGAGACgtaagctatt-tactgttgtggttg----aactctttctaagtgttttcttgtttcc--tgtttttgttttttcag------------------------

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|33796313|gb|CF324024.1|CF324024
EST:     ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC                         GTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
genomic: ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
EST: gi|88261690|gb|CI365266.1|CI365266
EST:     ACAGATGAAGAAAATGATATGCTTGACCTGGCATTTGGACTTACAGAAAC                         GTCTCGTCTTGGCTTTCAAGTGATAGCAAAGCCAGAACTTGATGGGCATGC
genomic: ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGAT-GGCATGC
EST: gi|88459335|gb|CI517013.1|CI517013
EST:     ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC                         GTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
genomic: ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
EST: gi|88288335|gb|CI515479.1|CI515479
EST:     ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC                         GTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
genomic: ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
EST: gi|10794608|gb|AU108574.1|AU108574
EST:     ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC                         GTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
genomic: ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
EST: gi|218490073|gb|FG948574.1|FG948574
EST:     ACAGATGAA-AAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC                         GTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
genomic: ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
EST: gi|88459059|gb|CI514340.1|CI514340
EST:     ATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC                         GTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
genomic: ATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
EST: gi|88459235|gb|CI516913.1|CI516913
EST:     CAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC                         GTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
genomic: CAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
EST: gi|88545049|gb|CI474579.1|CI474579
EST:     ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC                         GTCTCTTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
genomic: ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
EST: gi|33680136|gb|CF308375.1|CF308375
EST:     ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC                         GTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
genomic: ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
EST: gi|24468825|gb|CA305774.1|CA305774
EST:     ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC                         GTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
genomic: ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
EST: gi|88304282|gb|CI515555.1|CI515555
EST:     ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC                         GTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
genomic: ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
EST: gi|33680135|gb|CF308374.1|CF308374
EST:     ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC                         GTCTCGTCTTGGCTGTCAAGTGAT
genomic: ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGAT
EST: gi|88468585|gb|CI515067.1|CI515067
EST:     ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC                         GTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
genomic: ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
EST: gi|11443010|gb|BF430897.1|BF430897
EST:     ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAAC                         GTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG
genomic: ACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCG

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: 59 (upstream exon), 72 (downstream exon)
Score: 10

GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaag ... ctgtattcagGTCTCGTCTTGGCTGTCAAGTGATAGCAAAGCCAGAACTTGATGGCATGCGACTGGCATTACCAGCAGCTACACGAAACTTTGCGGTGGATGGCTTTGTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTAAATTATTATAATAAGCTAGAAGATCCAACAGATGAAGAAAATGATATGCTTGACCTTGCATTTGGACTTACAGAAACgtaagtgaagatatcttgaaggttttattaatttggcttatccagtttcatggttccgtggtgcttgctgtctgattatcgtgcaaacaagaatgttggg

- - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - AAGAAA