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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATTCTGGATAACCGAATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattccccctgctttttccatcacattgttctatctatgcgattgcttttctgaaggtgatccgattcgcatttcgcag

Basic information

species Oryza sativa
transcript LOC_Os01g17180.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g17180.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G132804_T01 (Zea mays), 5'ss of exon 11
CAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATTCTGGATAACCGAATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattccccctgctttttccatcacattgttctatctatgcgattgcttttctgaaggtgatccgat------tcgcatttcgcag
| || |||||||| |||||||| ||||| || ||||| ||||| ||||||||||| ||||||||||| ||||| |||||||| ||||| ||||| || ||||| |||  |||||    ||      |   ||  |  | | || | ||   |  |  |       || |||      | |  | | ||||
CGGAGAAGGATGTGGAGCAGCTGTTGGTATCGCTCATCCTGGACAACCGAATCCAAGGCCACATAGACCAGGTCAACAAGTTGCTAGAGCGTGGAGAGAGgtgtgtagcccccccaacttgatttccctgttaattcagc-atactatacttcgtgcggtcagattcagatattgtatggtttcttgcag

upper sequence: LOC_Os01g17180.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 11
CAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATTCTGGATAACCGAATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattccccctgctttttccatcacattgttcta-tctatgcgattgcttttctgaaggtgatccgattcgcatttcgcag
|||||||||||||||||||||| ||||| |||||||||||||| ||||| ||||| ||||||||||||||||| |||||| | ||||||||||| || ||||||  |   |||    ||| |  |  ||  |  | || | | |||| |    ||   || | ||||  | || || | | ||||
CAGAAAAGGATGTCGAGCAGCTGTTGGTGTCACTCATTCTGGACAACCGTATCCAAGGCCACATAGATCAGGTTAACAAGCTGCTAGAACGTGGAGAAAGgtgcagagcgcccaacttttctttaatactgtactgtactttgtgcggtcagattga-gatgttgatttgtttggcttgttgcag

upper sequence: LOC_Os01g17180.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 11
CAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATTCTGGATAACCGAATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattccccctgctttttccatcacat-tgttctatctatgcgattgcttttctgaaggtgatccgattcgcatttcgcag
||||  | ||||| |||||||| ||||| || || ||| ||||||||||||| || || || || ||||| ||||||   ||| |||| |||||||||||||     |||    |  |||||       || |||| |   | |    ||  | || |  |  |      ||    |||   |||
CAGAGGAAGATGTTGAGCAGCTGTTGGTGTCGCTGATTTTGGATAACCGAATTCAAGGGCATATTGATCAAGTGAACCGATTATTAGAGCGTGGTGACAGgttgagtttcatttttttttttattgattatctgttgttgttgtatcgttaatattatttaccttggtttatct--attgtccag

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|66919508|gb|CX106356.1|CX106356
EST:     ATCCANGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88416368|gb|CI540909.1|CI540909
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88553514|gb|CI483630.1|CI483630
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88538051|gb|CI467047.1|CI467047
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88848981|gb|CI087503.1|CI087503
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88551721|gb|CI481803.1|CI481803
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|58694676|gb|CK083363.1|CK083363
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88445960|gb|CI549683.1|CI549683
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|87026033|gb|CI250049.1|CI250049
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88458926|gb|CI555607.1|CI555607
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88542684|gb|CI472028.1|CI472028
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88464675|gb|CI534812.1|CI534812
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88450658|gb|CI547158.1|CI547158
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88523107|gb|CI450909.1|CI450909
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88248988|gb|CI248837.1|CI248837
EST:     CCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: CCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88246436|gb|CI246285.1|CI246285
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88525912|gb|CI452953.1|CI452953
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|86849423|gb|CI299644.1|CI299644
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|86487402|gb|CI130035.1|CI130035
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|86426049|gb|CI071146.1|CI071146
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTATTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|86831610|gb|CI301460.1|CI301460
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|15853965|gb|BI806761.1|BI806761
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88551722|gb|CI481804.1|CI481804
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|89161899|gb|CI102247.1|CI102247
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88902713|gb|CI088251.1|CI088251
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88481305|gb|CI418576.1|CI418576
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|163927941|gb|EG713517.1|EG713517
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
EST: gi|88297119|gb|CI545209.1|CI545209
EST:     ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAG                         GTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT
genomic: ATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCT

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: 71 (upstream exon), 73 (downstream exon)
Score: 46

CAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATTCTGGATAACCGAATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattc ... catttcgcagGTCGAAGGGAATGAGGAAATACCAAGCCATAGACAAGTGGAATACTCAGCTGAAGAACATCTACCAAACGGTGTCCAACAGAGTTGGGTGAGAGAGATAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAAAAGGATGTCGAGCAGCTCTTGGTCTCACTCATTCTGGATAACCGAATCCAGGGCCACATAGATCAGGTGAACAAGTTACTAGAACGTGGTGACAGgtgcgtattccccctgctttttccatcacattgttctatctatgcgattgcttttctgaaggtgatccgattcgcatttcgcag

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