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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagatctaacatacacatacctgtttttataggatgtgtggttggtcatgtatgtttttcttccccataagagaatttttaatcatgcatgccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG

Basic information

species Oryza sativa
transcript LOC_Os05g06430.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G110742_T02 (Zea mays), 3'ss of exon 7
tagatctaacatacacatacctgtttttataggatgtgtggttggtcatgtatgtttttcttccccataagagaatttttaatcatg-catgccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG
                                                 |||||  ||  | |    | | |  || |||||| ||   || || || ||| ||||| |||||||||||||| |||||||| |||||||| |||||||||||||| ||||||||||||||||| || || || ||||||||||| ||||||
-------------------------------------------------gtatgcattcttccatgttcacaacatctttaataataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G008647_T02 (Zea mays), 3'ss of exon 4
tagatctaacatacacatacctgtttttataggatgtgtggttggtcatgtatgtt-tttcttccccata-agagaatttttaatcatg-catgccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG
 | |   | |||    |    | |   |||   |  |     |    |||| |||  ||||||||   |  | || || |||||| ||   || || || ||| ||||| |||||| ||||||| |||||||| |||||||| |||||||||||||| ||||||||||||||||| || || || ||||||||||| ||||||
caaa---agcatctttaataatatacctatgacaatttataataactatgtttgtcctttcttccatgttcacagcatctttaataataatatacctctgcagATATGGTGTTTCTAGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G170845_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------------------------------tagatctaacatacacatacctgtttttataggatgtgtggttggtcatgtatgtttttcttccccata---agagaatttttaatcatg-catgccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG
                                                                                            | | |   | | ||  |    |  ||   |   ||| ||         | |      |    ||    | || || |||||| ||   || || || ||| ||||| |||||||||||||| |||||||| ||||  || |||||||||||||| ||||||||||||||||| || || || ||||||||||| ||||||
gtatgcattctgacttgtctatttcagtggttgttatgcacattagctttcagcctttagtttaacaccactggattttcttatattacgattgtgatgaaaaaatttcctcatgaatcacagaagtgattctctcgtcgtttgacagatatggatgttcacagcatctttaataataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTATCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G159369_T01 (Zea mays), 3'ss of exon 7
---tagatctaacatacacatacctgtttttataggatgtgtggttggtcatgtatgtt-tttcttccccata-agagaatttttaatcatgcatgccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG
    ||| ||   |   | | ||      |   |  || | |  |     | || |||  ||||||||   |  | || || |||||| ||  || || || ||| ||||| |||||||||||||| |||||||| |||||||| |||||||||||||| ||||||||||||||||| || || || ||||||||||| ||||||
tgacaga-ctgttagggata-acacaacctatgacaatttataat-aactacgtttgtcctttcttccatgttcacagcatctttaataat--atacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G404011_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------------------------------------------tagatctaacatacacatacct---gtttttatagga-tgtgtggttggtcatgtatgtttttcttccccataagagaatttttaatcatg-catgccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG
                                                                                            | | |   | | ||  |    |   | | || | ||  |   | ||| | |       | |      | | |  || |||||| ||   || || || ||| ||||| |||||||||||||| |||||||| |||||||| |||||||||||||  ||||||||||||||||| || || || ||||||||||| ||||||
gtatgcattctgacttgtctatttcagtggttgttatgcacattagctttcagcctttagtttaacaccattggattttcttatatggcgattgtgatgaaaaaatttcctcaggaatcacagaagtgattctctcgtcgtttg-acagatatggatgttcacaacatctttaataataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGTCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AC217311.3_FGT007 (Zea mays), 3'ss of exon 1
tagatctaacatacacatacctgtttttataggatgtgtggttggtcatgtatgtttttcttccccataagagaatttttaatcatg-catgccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG
                                                 |||||  ||  | |    | | || || |||||| ||   || || || ||| ||||| |||||||||||||| |||||||| |||||||| |||||||||||||| ||||||||||||||||| || || || ||||||||||| ||||||
-------------------------------------------------gtatgcattcttccatgttcacagcatctttaataataatatacctctgcagATATGGTGTTTCTGGTTTCCCTACATTGAAGTTCTTCCCTAAGGGAAACAAAGCCGGTGAAGATTATGATGGTGGCCGGGACTTGGATGACTTTGTCAAG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA02G01750.3 (Glycine max), 3'ss of exon 7
-tagatctaacatacacatacctgtttttataggatgtgtggttggtcatgtatgtttttcttccccataagagaatttttaatcatgcatgccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG
 ||        |   | | |     |          |  |    | |    |||       |     ||||  ||| |||     |   ||     | ||||||||  ||   ||| || || || ||||| |||||||||||||| ||||||||||||||||| || |  || ||  | || ||||||||||| ||    
ttacggtggttaagaaaacaaaaaatccagcgaagaggataaa-gatggaatattacaacatgataaataattgaagtttgctggaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G01820.1 (Glycine max), 3'ss of exon 8
tagatctaacatacacatacctgtttttataggatgtgtggttggtcatgtatgtttttcttccccataagagaatttttaatcatgc----atgccactt---cagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG
         ||||    |     |||  |       |||| | |   || || |  |   | |  ||| | | |   || ||   |||    ||   | ||   |||||| |  ||   ||| || || || ||||| |||||||||||||| ||||||||||||||||| || |  || ||  | || ||||||||||| ||    
-----tattcatagttgtcttcctttcaagtcataatgtgatgga--atatacgaatcgttacaacatgataaataattgaagtttgctggaataatatttatgcagGTACGACGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGACTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G39130.1 (Glycine max), 3'ss of exon 7
tagatctaacatacacatacctgtttttataggatgtgtggttggtcatgtatgtttttcttccccataagagaatttttaatcatgcatgccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG
  |     |||   ||||     ||| | |   || |    | |||        | |||         | | |  |  || |  |    | ||| | ||| ||||| |||  ||| |  || ||| |||| || ||||||||| | ||||||||||||||||||||| |||| || || || |||||||| || ||    
--gtgagtacagtgacattttgatttatcttctatttaaactaggtggatatcatatttaagaaatgcatgtgcctaatttagaaaattttccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA06G24520.1 (Glycine max), 3'ss of exon 9
-tagatctaacatacacatacctgtttttataggatgtgtggttggtcatgtatgtttttcttccccataagagaatttttaatcatgcatgccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG
 ||        |   | | |     |          |  |    | |    |||       |     ||||  ||| |||     |   ||     | ||||||||  ||   ||| || || || ||||| |||||||||||||| ||||||||||||||||| || |  || ||  | || ||||||||||| ||    
ttacggtggttaagaaaacaaaaaatccagcgaagaggataaa-gatggaatattacaacatgataaataattgaagtttgctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 7
tagatctaacatacacatacctgtttttataggatgtgtggttggtcatgtatgtttttcttccccataag-agaatttttaatcatgcatgccac-ttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG
      |||  |  |||  | | || |||       | |   || | |      ||| | || |  | ||  | ||  |  |  || | |    |  ||||| ||||||||   ||| ||||| ||||||||||||||||||||||  |||||||||||| | |||||||| || ||  | || || |||||||| || |  
-----gtaagttggacaggcattttattaataccgattttactgtttaaagtcatttatgtttcataaaaccaaaacataaagacaagtaccttatattcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC

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|27577315|gb|CB000010.1|CB000010
EST:     GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA                         GTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
genomic: GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAAgtatgctttc ... gccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
EST: gi|58653948|gb|CK042628.1|CK042628
EST:     GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA                         GTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
genomic: GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAAgtatgctttc ... gccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
EST: gi|58676547|gb|CK065234.1|CK065234
EST:     GCTGACAAACACACTGCC-TGGCAGAGAA                         GTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
genomic: GCTGACAAACACACTGCCTTGGCAGAGAAgtatgctttc ... gccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
EST: gi|58659841|gb|CK048521.1|CK048521
EST:     GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA                         GTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
genomic: GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAAgtatgctttc ... gccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
EST: gi|58690891|gb|CK079578.1|CK079578
EST:     GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA                         GTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
genomic: GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAAgtatgctttc ... gccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
EST: gi|12622813|gb|AU173026.1|AU173026
EST:     GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA                         GTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
genomic: GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAAgtatgctttc ... gccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
EST: gi|163927756|gb|EG710536.1|EG710536
EST:     GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA                         GTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
genomic: GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAAgtatgctttc ... gccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
EST: gi|27577494|gb|CB000189.1|CB000189
EST:     GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA                         GTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
genomic: GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAAgtatgctttc ... gccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
EST: gi|58683615|gb|CK072302.1|CK072302
EST:     GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAA                         GTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
genomic: GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAAgtatgctttc ... gccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
EST: gi|58675064|gb|CK063751.1|CK063751
EST:     GTTGTTATTGCCAATCTTGATGCTGACAAACAGACTGCCTTGGCAGAGAA                         GTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA
genomic: GTTGTTATTGCCAATCTTGATGCTGACAAACACACTGCCTTGGCAGAGAAgtatgctttc ... gccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgtatgtttttcttccccataagagaatttttaatcatgcatgccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG
                               ttttaat  putative branch site (score: 3)
                                              ccacttc  putative PPT
                     ataagagaatttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagatctaacatacacatacctgtttttataggatgtgtggttggtcatgtatgtttttcttccccataagagaatttttaatcatgcatgccacttcagGTATGGAGTTTCTGGTTTCCCCACATTGAAATTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGGTCGCGAGTTGGATGACTTCGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA