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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtttttgtttttcgtttgaattttgttttttatcatgttttccaagcaatggatgtttttggctaaagttaataagttattacatgtattgttgacagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCACTAGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGTTTCTTTGCAA

Basic information

species Oryza sativa
transcript LOC_Os01g55360.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55360.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G825110_T01 (Zea mays), 3'ss of exon 8
----ctgtttttgtttttcgtttgaattttgttttttatcatgttttccaagcaatggatgtttttggctaaagttaataagttattacatgtattgttgacagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCACTAGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGTTTCTTTGCAA
     || || |||  |   |    |||  |||||   | || | ||   ||   |  |  | ||||  |     |  |   | ||||| |||  | || ||||||||| ||||| ||  | |   || ||||||||||||||||||||||||| |||||||| ||||| |||||||||||||| || ||||| || ||||| |
atgtttgattgtgtactctatcatcattg-gttttgcgttatctctttagagtt-tctagatgtttgatttgtactc-tgtttgattacgtgt-ctcttaacagTTCCCATGGAAAGATCTAGCCATTATGCCTGTGCAGTGGCATGCTTTAGCCCTAGGTTTATTTGCGTCAATAATAGCACCATTCGGAGGATTTTTTGCGA

upper sequence: LOC_Os01g55360.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G452529_T02 (Zea mays), 3'ss of exon 8
ctgtttttgtttttcgtttgaat--tttgttttttatcatgttttccaagcaa-tggatgtttttggctaaagttaataagttattacatgtattgttgacagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCACTAGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGTTTCTTTGCAA
 | | |||  | | |      ||  || |||||  || || |||    ||    | |||||||     |  | |   |  |  | |||||   || || ||||||||| ||||| ||| | | | || ||||||||||||||||||||||||| |||||||| |||||||||||||||||||| |||||||| || ||||| |
-tatatttaatgtaccacatcatcattggttttgcattatctttctagagtttctagatgtttgattttgtactctgtttg--aatacatcgtttcttaacagTTCCCATGGAAAGAACTAGCTATTATGCCTGTGCAGTGGCATGCTTTAGCCCTAGGTTTATTTGCATCAATAATAGCACCATTTGGAGGATTTTTTGCGA

upper sequence: LOC_Os01g55360.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 8
-------ctgtttttgtttttcgtttgaattttgttttttatcatgttttccaagcaatggatgtttttggctaaagttaataagttattacatgtattgttg-acagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCACTAGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGTTTCTTTGCAA
         ||     || |   ||     |  | |    |||  | || |     || |  ||         | |  | |  |   |||| |||   | ||   |||||  ||||||| ||  |     |  | ||  | || |||||| |||||   ||||| |||||||| ||||| || |||||||||||||| ||||||||||
aataaaaaagtgaccattctgtattca---tgagatgccaatctagattcctgg--aacgtctgaa---aatcataacttacgacccattatatgctgtcttatgcagTTTTCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGTCTAGGCTTGTTTGCTTCAATTATTGCACCTTTTGGAGGCTTCTTTGCAA

upper sequence: LOC_Os01g55360.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 8
ctgtttttgtttttcgtttgaattttgttttt-tatcatgttt-tccaagcaatggatgtttttgg---ctaaagttaataagttattacatgtattgttg-acagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCACTAGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGTTTCTTTGCAA
         |     ||    ||| ||| ||  |   ||| |  ||||       |     | ||      | |  | |  |   | || ||||  | ||  ||||||  ||||||| ||  |     |  | ||  | || |||||| |||||   || || |||||||| ||||| || |||||||||||||| ||||||||||
------cattaaaaagtgaccattctgtattcatgagatgctaatccagattcctggaacgtctgaaaatcataacttacgacccactatatgttgtcttatacagTTTGCTTGGAAAGAGATATCAATCCTACCAATTCAATGGCATTCTTTATGTCTTGGCTTGTTTGCTTCAATTATTGCACCTTTTGGAGGCTTCTTTGCAA

upper sequence: LOC_Os01g55360.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 8
ctgtttttgtttttcgtttgaattttgttttttatcatg---ttttccaagcaat--ggatgtttttggctaaagttaataagttattacatgtattgttgacagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCACTAGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGTTTCTTTGCAA
    | |||||        ||   | || ||  |   ||   ||  ||   |  |  | ||  | |||  | | |||  | |  | |    |  |||  || ||||| |||||||||||| |     |  | ||||| |||||||||||||||   || |||||||| || ||||| ||||||||||||||||| || || || |
----tcttgttagctaacagatagtagtgttagactgtgcggttagcctttctgtttgaataatattgcatgaggtttctcaactttctagttcatttgtg-cagTTTCCTTGGAAGGAAATGACGATCCTCCCTGTTCAGTGGCATGCTTTATGCCTCGGTTTGTTCGCTTCAATCATAGCACCTTTTGGAGGATTTTTCGCTA

upper sequence: LOC_Os01g55360.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv00s0598g00010.t01 (Vitis vinifera), 3'ss of exon 9
ctgtttttgtttttcgtttgaattttgttttttatcatgttttccaagca-atggatgtttttggctaaagttaataagttattacatgtattgttg-acagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCACTAGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGTTTCTTTGCAA
 |||    | | ||| | ||| |   |  |   ||     ||| ||| |  |   |     |  |  |   |       |   | |   |  | |||  ||||| ||||||||||| ||     |||| || || |||||||||||||||    | ||||||||||||||||||||||||||||||||||| || |||||||
-tgtaaa-gctattcctctgattaaagcatgggatttaaattttcaatctcaaaaaaaagatcagtaactctctccctctctcttctcattctcttgtgcagTTTCCTTGGAAGGAGGTCTCCATTTTACCAGTTCAGTGGCATGCTTTATGTGTCGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGATTTTTTGCAA

upper sequence: LOC_Os01g55360.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv19s0090g01220.t01 (Vitis vinifera), 3'ss of exon 7
-ctgtttttgtttttcgtttgaattttgttttttatcatgttttccaagcaatggatgtttttggctaaagttaataagttattacatgt-attgttgacagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCACTAGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGTTTCTTTGCAA
  ||| |   | |   | | |  ||   |   |  |  |    |  ||   ||| ||| | ||    | |   ||| |  |||     || ||   |  ||||| |||||||| ||  ||    ||||||| ||||||||||||||||||    | ||||||||||||||||| |||||||| ||||| || || ||||| |
cttgtgtaaatatgcaggtaggtttcactccctctttttaacctttaatttatgcatggtgtttatcagaa--aattaactatgtttggtgataacttgcagTTTCCTTGGAAAGAGATTTCAGTTTTGCCGGTGCAGTGGCATGCTTTATGCTTGGGTTTGTTTGCATCAATTATAGCACCCTTTGGTGGCTTTTTTGCTA

upper sequence: LOC_Os01g55360.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 8
ctgtttttgtttttcgtttgaattttgttttttatcatgttttccaagca-atggatgtttttggctaaagttaataagttattacatgtattgttg-acagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCACTAGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGTTTCTTTGCAA
 |||    | | ||| | ||| |   |  |   ||     ||| ||| |  |   |     |  |  |   |       |   | |   |  | |||  ||||| ||||||||||| ||     |||| || || |||||||||||||||    | ||||||||||||||||||||||||||||||||||| || |||||||
-tgtaaa-gctattcctctgattaaagcatgagatttaaattttcaatctcaaaaaaaagatcagtaactctctccctctctcttctcattctcttgtgcagTTTCCTTGGAAGGAGGTCTCCATTTTACCAGTTCAGTGGCATGCTTTATGTGTCGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGATTTTTTGCAA

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|29671303|gb|CB667578.1|CB667578
EST:     CTATGTTTAAGCCAGAACATTATTCTTTGGGAGAATGGGTGCCAAAGGGG                         TTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCA
genomic: CTATGTTTAAGCCAGAACATTATTCTTTGGGAGAATGGGTGCCAAAGGGGgtaagaacat ... ttgttgacagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCA
EST: gi|29679198|gb|CB675473.1|CB675473
EST:     CTATGTTTAAGCCAGAACATTATTCTTTGGGAGAATGGGTGCCAAAGGGG                         TTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCA
genomic: CTATGTTTAAGCCAGAACATTATTCTTTGGGAGAATGGGTGCCAAAGGGGgtaagaacat ... ttgttgacagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCA
EST: gi|29681975|gb|CB678250.1|CB678250
EST:     CTATGTTTAAGCCAGAACATTATTCTTTGGGAGAATGGGTGCCAAAGGGG                         TTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCA
genomic: CTATGTTTAAGCCAGAACATTATTCTTTGGGAGAATGGGTGCCAAAGGGGgtaagaacat ... ttgttgacagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCA
EST: gi|29671304|gb|CB667579.1|CB667579
EST:     CTATGTTTAAGCCAGAACATTATTCTTTGGGAGAATGGGTGCCAAAGGGG                         TTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCA
genomic: CTATGTTTAAGCCAGAACATTATTCTTTGGGAGAATGGGTGCCAAAGGGGgtaagaacat ... ttgttgacagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcaatggatgtttttggctaaagttaataagttattacatgtattgttgacagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCACTAGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGTTTCTTTGCAA
                    taaagttaataagtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtttttgtttttcgtttgaattttgttttttatcatgttttccaagcaatggatgtttttggctaaagttaataagttattacatgtattgttgacagTTCCCTTGGAAGGAAGTTGTTCTTTTGCCTGTGCAGTGGCATGCTTTAGCACTAGGTTTGTTTGCATCAATAATAGCACCTTTTGGAGGTTTCTTTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG