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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttccttaccttattatggttcacctggaagaatgtagcttttgcttaattaacaatatttttcaatgctgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACTTCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA

Basic information

species Oryza sativa
transcript LOC_Os03g61810.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g61810.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G840909_T02 (Zea mays), 3'ss of exon 4
gttagttccttaccttat-tatggttcacctggaagaatgta----gcttttgcttaattaacaatatttttcaatgctgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACTTCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA
|||  || |||| ||||  |||  ||||  ||  ||||| ||    || | |   | || | |||| || |||||||||| | ||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||||||| | || |||||||  ||||| ||||||||||
gttgatttcttaacttacatattcttcatatgatagaatatatggagcatgttactgat-agcaatcttgttcaatgctgtactgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCAATTGCCATTGGATTTGATGATTTCATTGCTGATGCTCTCAGAGGAACTGGGTACTATCAGAAGGCCA

upper sequence: LOC_Os03g61810.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G20970.2 (Glycine max), 3'ss of exon 4
-----------------gttagttccttaccttattatggttcacctggaagaatgtagcttttgcttaattaacaatatttttcaatgctgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACTTCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA
                 | |||           ||||   ||    |  ||   |    ||   ||  | ||    | | | |||| |      ||  ||||| |||| |||||||| |||||||| || || ||||| ||||||||||||||||||||| | ||||| ||| | || ||||  | ||||||||| ||  
atttaaaaatctttaaagatagagtacatgaaaattaaatttattttacaatgcttactctcgggcacactttcttacaatattcactttatttatatagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGATTCGATGACTTCATTTCAGATGCATTGCGAGGCACTGGATTCTACCAGAAAGCAC

upper sequence: LOC_Os03g61810.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G09440.1 (Glycine max), 3'ss of exon 4
-gttagttcct----taccttattat--ggttcacctggaagaatgtagctt-ttgcttaattaacaatattttt-caatgctgcaat--------gcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACT-TCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA
  ||  | | |    ||| | |  ||     | |  ||  | | || ||||| || |||      | |  || ||   |  ||  |||          ||||| |||| |||||||| |||||||| || || ||||| |||||||||||||||| | ||| | ||||| ||| | || ||||  | ||| ||||| ||  
tttttatacttaaaatacatgaaaattaaacttatttgacaaattgaagcttattacttttgggcccactttcttgtcacactcaaattattttttatagAGGTTGGTTTATGGAGCGAAGGCAGAGGCAGCAATTGCTATTGGATTCGATGACTATGATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAAGCA-

upper sequence: LOC_Os03g61810.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G22830.1 (Glycine max), 3'ss of exon 8
--------------gttagttccttaccttattat--ggttcacctggaagaatgtagcttttg-cttaattaacaatatttttcaatgctgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACTTCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA
                   |    ||| | |  ||    ||||  |   |     ||   |  | |  | ||    | | | |||| |      ||  ||||| |||| |||||||| |||||||| ||||| ||||| ||||||||||||||||||||| | ||||| ||| | || ||||  | ||||| ||| ||  
atttaaaaatctttaaagatagagtacatgaaaattaaattcattttacaatgcttactctcgggcacattttcttacaatattcactttatttatatagAGGTTGGTTTATGGAGCAAAGGCAGAGGCTGCAATTGCTATTGGATTCGATGACTTCATTTCAGATGCATTGCGAGGCACTGGATTCTACCTGAAAGCAC

upper sequence: LOC_Os03g61810.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G12900.1 (Glycine max), 3'ss of exon 2
------gttagttccttaccttattatggttcacctggaagaatgtagcttt---tgcttaatta-----acaatatttttcaatgctgca---atgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACTTCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA
      | || || || |     | ||  | || |   |   |  ||  ||    || ||| ||      ||| | |||| ||||  |  |   || |||||| |||| |||||||| |||||||| || || ||||| ||| | ||||||||||||||| | ||||| ||| | || ||||| | ||| ||||||||  
atttaagataatttctaattaattaatattacatcaaaattgaattattttacaatgattacttttgggcacacttttttacaatattaaatttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTAGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGCATTCTATCAGAAGGCAC

upper sequence: LOC_Os03g61810.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA20G37210.1 (Glycine max), 3'ss of exon 4
----------gttagttccttacc-ttattatggttcacctggaagaa-----tgtagcttttgcttaattaacaatatttttcaatgctgcaatg-----cagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACTTCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA
          |  |   ||  ||  ||  |||  | | |     | |      | |||  |||  | || | |  | ||| |||| | ||   |       ||||| ||||| || ||||| || ||||||||||| || || |||||||| ||||| |||||||| |||||  ||||||| |||| ||  || ||||||||  
gtgagcctctgccacagccacactattcatattttcctctcaccacatgtttctctagtatttattaaaatgatcacattgttcattcctttcacatcaaacagAGACTGGTTTACGGAGCTAAAGCAGAAGCTGCAATAGCAATTGGATTTGATGATTTCATTGCCGATGCACTGAGGGGCACTGGTTTTTATCAGAAGGCTC

upper sequence: LOC_Os03g61810.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G09430.2 (Glycine max), 3'ss of exon 3
------gttagttccttaccttattatggttcacctggaagaatgtagcttt---tgcttaatta-----acaatatttttcaatgctgca---atgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACTTCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA
      | || || || |     | ||  | || |   |   |  ||  ||    || ||| ||      ||  | | || ||||  |  |   || |||||| |||| |||||||| |||||||| || || ||||| ||||| ||||||||||||||| | ||||| ||| | || ||||  | ||| ||||||||  
atttaagataatttctaattaattaatattacatcaaaattgaattattttacaatgattacttttgggcacgctttcttacaatattaaatttatacagAGGTTGGTTTATGGAGCAAAGGCAGAGGCAGCAATTGCTATTGGGTTCGATGACTTCATTTCAGATGCATTGCGAGGTACTGGATTCTATCAGAAGGCAC

upper sequence: LOC_Os03g61810.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G28050.2 (Arabidopsis thaliana), 3'ss of exon 5
------gttagttccttaccttattatgg-ttcacctggaagaatgtagcttttgcttaattaacaatatttttcaatgctgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACTTCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA
        | |   |    ||  | |      || ||     |   |  | |||     | | |  |    | ||  | ||   |  |||||| |||| ||||||||||| || ||||| ||||| ||||| || || ||||||||||| |||||||||||||| || || |     ||||||||  | |
gtaagatgtcgaaacaagtctactcacaaacccatctttctaatcatttcatttatcacaatgagtactcatgtctctacttgtaaacagAGGTTGGTTTATGGAGCCAAAGCCGAAGCAGCTATAGCCATCGGGTTTGATGACTTCATAGCTGATGCTTTGAGAGGCACGGGGGTTTACCAGAAATCTA

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|58691571|gb|CK080258.1|CK080258
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|88555582|gb|CI485850.1|CI485850
EST:     TTTCGGCGCTNTGCATCTATCACGGATTAAG                         AGGCTGGTTTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: TTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|86526937|gb|CI167143.1|CI167143
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|88530960|gb|CI459394.1|CI459394
EST:     TGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: TGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|88842879|gb|CI371779.1|CI371779
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|88554790|gb|CI484994.1|CI484994
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|27547275|gb|CA765405.2|CA765405
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|66916794|gb|CX103642.1|CX103642
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|88526990|gb|CI455094.1|CI455094
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|89167816|gb|CI021515.1|CI021515
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|58688225|gb|CK076912.1|CK076912
EST:     GTGAACCTTGCCCACTGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AAGCTGGTGTATGGAGCCAAAGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|25806978|gb|CA762939.1|CA762939
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|88466860|gb|CI539656.1|CI539656
EST:     CCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: CCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT

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: 60 (upstream exon), 65 (downstream exon)
Score: 19

CAAAAAGCTTGGAAAAATTGAGTTGTCAGACTGTGAAATGTATGCATCATGTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACTTCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggaagaatgtagcttttgcttaattaacaatatttttcaatgctgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACTTCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA
                       aattaac  putative branch site (score: 19)
               ttttgcttaattaaca  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttccttaccttattatggttcacctggaagaatgtagcttttgcttaattaacaatatttttcaatgctgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACTTCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT