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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgagttccccccacgtcaattcacaaacaactgaccaatttcaattgcagtatctgctcttattgtgcacaaactcaaacaattcataacattgtgattttattttag

Basic information

species Oryza sativa
transcript LOC_Os12g03060.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03060.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G080404_T01 (Zea mays), 5'ss of exon 2
CTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgagttccccccacgtcaattcacaaacaactgaccaatttcaattgcagt-atctgctcttattgtgcacaaactcaaacaattcataacattgtgattttattttag
|   ||||||||  |||| ||  | ||| | || || ||| | ||  ||||||||||||  ||||||||||| ||||||||||| |||||||||||  |||| |||            | || ||  |  || |       ||| |||  ||| | | |||  |||||    || |  || |  |   |   ||  |||  |  | || | ||||
CAGCTCTGATGATGCTAAGGAGGTAGTCCATTACCAAACAATCTCATCAAAGAGCTTAGCTAAATCTGTTCTCGAGGAAGGTGGCTGGTCAAACTTCATGgtaagtatcacgttggtgaagtgaaa-cttaagctctcatgcaacttcttttgaaattatcaactcttgcattgaaacaagttcactgaccgatgtcatgattttcttttcttag

upper sequence: LOC_Os12g03060.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G179737_T02 (Zea mays), 5'ss of exon 3
CTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgagttccccccacgtcaattcacaaacaactgaccaatttcaattgcagt-atctgctcttattgtgcacaaactcaaacaattcataacattgtgattttattttag
|   ||||||||  |||| ||  | ||| | || || ||| | || |||||||||||||  ||||||||||| ||||||||||| |||||||||||  |||| |||            | ||  |  |  || |       ||| |||  ||| | | |||  |||||    || |  || |  |   |   ||  |||  |  | || | ||||
CAGCTCTGATGATGCTAAGGAGGTAGTCCATTACCAAACAATCTCACCAAAGAGCTTAGCTAAATCTGTTCTCGAGGAAGGTGGCTGGTCAAACTTCATGgtaagtatcacattggtgaagtggaa-cttaagctctcatgcaacttcttttgaaattatcaactcttgcattgaaacaagttcactgaccgatgtcatgattttcttttcttag

upper sequence: LOC_Os12g03060.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G371679_T01 (Zea mays), 5'ss of exon 4
CTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgagttccccccacgtcaattcacaaacaactgaccaatttcaattgcagt-atctgctcttattgtgcacaaactcaaacaattcataacattgtgattttattttag
|   ||||||||  |||| ||  | ||| | || || ||| | || |||||||||||||  ||||||||||| ||||||||||| |||||||||||  |||| |||            | || ||  |  || |  ||   ||| |||  ||| | | |||  |||||    || |  || |  |   |   ||  |||  |  | || | ||||
CAGCTCTGATGATGCTAAGGAGGTAGTCCATTACCAAACAATCTCACCAAAGAGCTTAGCTAAATCTGTTCTCGAGGAAGGTGGCTGGTCAAACTTCATGgtaagtatcacattggtgaagtgaaa-cttaagct-ctatgcaacttcttttgaaattatcaactcttgcattgaaacaagttcactgaccgatgtcatgattttcttttcttag

upper sequence: LOC_Os12g03060.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G410155_T01 (Zea mays), 5'ss of exon 2
CTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgagttccccccacgtcaattcacaaacaactgaccaatttcaattgcagt-atctgctcttattgtgcacaaactcaaacaattcataacattgtgattttattttag
|   ||||||||  |||| ||  | ||| | || || ||| | || |||||||||||||  ||||||||||| ||||||||||| |||||||||||  |||| |||            | || ||  |  || | |     ||| |||  ||| | | |||  |||||    || |  ||||  |   |   ||  |||  |  | || | ||||
CAGCTCTGATGATGCTAAGGATGTAGTCCATTACCAAACAATCTCACCAAAGAGCTTAGCTAAATCTGTTCTCGAGGAAGGTGGCTGGTCAAACTTCATGgtaagtatcacgttggtgaagtgaaa-cttaagctatcatgcaacttcttttggaattatcaactcttgcattgaaacaacttcactgaccgatgtcatgattttcttttcttag

upper sequence: LOC_Os12g03060.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G017941_T01 (Zea mays), 5'ss of exon 3
CTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgagttccccccacgtcaattcacaaacaactgaccaatttcaattgcagtatctgctcttat-tgtgcacaaactcaaacaattca-taacattgtgattttattttag---
|   ||||||||  |||| ||  | ||| | ||||| ||| | || ||||||| |||||  ||||||||||||||||||||||| ||||||| |||  |||| |||    | || |    |  | ||  |   ||        ||||   |   | ||||  |||||   ||    ||| || ||  | |||  | |  |  ||||||| | ||     
CCGCTCTGATGATGCTAAGGAGGTAGTCCATTATCAAACAATCTCACCAAAGAACTTAGCTAAATCTGTTCTTGAGGAAGGTGGCTGGTCAACCTTTATGgtaagt---atcccactggtgaaacttatctctcatgcagtttattt---tcaaattatcaactcttgcgtggaagcaagcttaataagttccctgatgtcatgattttctattcttag

upper sequence: LOC_Os12g03060.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G318871_T01 (Zea mays), 5'ss of exon 2
CTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgagttccccccacgtcaattcacaaacaactgaccaatttcaattgcagt-atctgctcttattgtgcacaaactcaaacaattcataacattgtgattttattttag
|   ||||||||  |||| ||  | ||| | || || ||| | || |||||||||||||  ||||||||||| ||||||||||| |||||||||||  |||| |||            | || ||  |  || |       ||| |||  ||| | | |||  |||||    || |  || |  |   ||  ||  |||  |  | || | ||||
CAGCTCTGATGATGCTAAGGAGGTAGTCCATTACCAAACAATCTCACCAAAGAGCTTAGCTAAATCTGTTCTCGAGGAAGGTGGCTGGTCAAACTTCATGgtaagtatcacgttggtgaagtgaaa-cttaagctctcatgcaacttcttttgaaattatcaactcttgcattgaaacaagttcactgatcgatgtcatgattttcttttcttag

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|29618674|gb|CB623686.1|CB623686
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|88415912|gb|CI594024.1|CI594024
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|88828089|gb|CI778654.1|CI778654
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|86904894|gb|CI310687.1|CI310687
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|33653554|gb|CF276168.1|CF276168
EST:     GAGCTTAGTGAAATCTGTTCTTGAGGAAGGTNGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAG-GTTTGATGTTGCAGTTCTTTTTCT
genomic: GAGCTTAGTGAAATCTGTTCTTGAGGAAGGT-GGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTT-GATGTTGCAGTTCTTTTTCT
EST: gi|58668824|gb|CK057510.1|CK057510
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|88736919|gb|CI760427.1|CI760427
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|88718196|gb|CI741706.1|CI741706
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAG
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAG
EST: gi|88337398|gb|CI629688.1|CI629688
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|86910179|gb|CI292983.1|CI292983
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|29657293|gb|CB653568.1|CB653568
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|66920771|gb|CX107619.1|CX107619
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|88356178|gb|CI627626.1|CI627626
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCGTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|25798686|gb|CA754647.1|CA754647
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|27576657|gb|CA999351.1|CA999351
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|88733588|gb|CI756765.1|CI756765
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGT
EST: gi|88402485|gb|CI596346.1|CI596346
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|29686826|gb|CB683101.1|CB683101
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|58597158|gb|CK007686.1|CK007686
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
EST: gi|88337316|gb|CI629606.1|CI629606
EST:     AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTG                         TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT
genomic: AGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTT

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), 69 (downstream exon)
Score: 44

CTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgag ... tttattttagTGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTGGTGgtgagttgagttccccccacgtcaattcacaaacaactgaccaatttcaattgcagtatctgctcttattgtgcacaaactcaaacaattcataacattgtgattttattttag

- - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT