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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttctaaagtgtgtgacaatactaggtaacgtaaaaagttagtacataaatagacgtgtttcctgtccaaattactcaacttcggtctgtgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACGTGGCATTATGTATGAAGCTCTTTGAGCACAAACCTTTTGATGCAAGGAC

Basic information

species Oryza sativa
transcript LOC_Os01g07310.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07310.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G081848_T05 (Zea mays), 3'ss of exon 2
----ggttctaaagtgtgtgacaatactaggtaacgtaaaaagttagtacataaatagacgtgtttcctgtccaaattactcaacttcggtctgtgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACGTGGCATTATGTATGAAGCTCTTTGAGCACAAACCTTTTGATGCAAGGAC
     || || |||||   | |  | |||   |||  | ||  |||| | | ||   |  |  ||||||    |   || | || |   || |   |||||||||||| |||||||||||||||||||| || || || || |||||||| || || |||||||||||||| |||||||||||||||||||| |||||||||||
cacgtgtcctcaagtgacagtccgt-ctata-aacagataatattagcaaagaag--gcaggttttcctccatatgctaataaaatctcgtattcattttgcagCCACCACTTTGACAAGCTGGCATCTTCTGGTCACCTTCTGCTCTCTCCATGTAGCATTATGTATGAAACTCTTTGAGCACAAACCTTTCGATGCAAGGAC

upper sequence: LOC_Os01g07310.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G116053_T01 (Zea mays), 3'ss of exon 2
-ggttctaaagtgtgtgacaatactaggtaacgtaaaaagttagtacataaatagacgtgtttcctgtccaaattactcaacttcggtctgtgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACGTGGCATTATGTATGAAGCTCTTTGAGCACAAACCTTTTGATGCAAGGAC
    | |   | | |||||| | |      |   | | | | |   || | |  |  |  ||||||       ||| | || |  ||| |   |||||||||||||||||||||||||||||||||||| |||||||| || ||||| || |||||||||||||||||||| ||||||||||||||||| |||||||||||
caagtgtggtgag-gtgacagtgcgtctataaacagataatgatagcaaagaaggcaggttttcctccaagtgttaataaaatgtggtattcattttgcagCCACTACTTTGACAAGCTGGCATCTCCTGGTTACATTCTGTTCTCTCCATGTGGCATTATGTATGAAGCTGTTTGAGCACAAACCTTTCGATGCAAGGAC

upper sequence: LOC_Os01g07310.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G14980.1 (Glycine max), 3'ss of exon 2
--ggttctaaagtgtgtgacaatactaggtaacgtaaaaagttagtacataaatagacgtgtttcctgtccaaattactcaacttcggtctgtgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACGTGGCATTATGTATGAAGCTCTTTGAGCACAAACCTTTTGATGCAAGGAC
    || |       ||  |   |    | | | |||    || | |    |||   |  |  |   |     | ||   | | | |   |      |||||| || ||||||||||| |||||||| || || |||||||| || ||||| |||||| ||    |||  || ||||||||||||||||||||    |   |
taacttttgttagaagtagctccatgctgcatcctaacccatttgaagtataatgtcctagagttgaggttttaatatgtatccttgaattcc--catgcagCTACAACTTTGACAAGTTGGCATCTTCTTGTAACATTTTGTTCCCTTCATGTGGCACTAAAGTTGAGACTTTTTGAGCACAAACCTTTTGAGCAGAAAGC

upper sequence: LOC_Os01g07310.4 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G30460.1 (Arabidopsis thaliana), 3'ss of exon 3
ggttctaaagtgtgtgacaatactaggtaacgtaaaaagtta-gtacataaatagacgtgtttcctgtcca-aattactca--acttcggtctgtgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACGTGGCATTATGTATGAAGCTCTTTGAGCACAAACCTTTTGATGCAAGGAC
   |||  |   || |  ||  | |   |   ||| |  ||| | |   ||    |     |  ||||    ||| | | |  ||||     ||   ||  |||| |||||||||||||||||||||||  | || |||||||| || ||||| ||||||||||| |||||| | ||||||||||| ||||||||| || |  |
---tctttaccatgggtgaactccattcatgataacagtttatgcatggaatctcatagtctatctgtgtgtaatcatttattactttatattgaactt-acagCAACTACTTTGACAAGCTGGCATCTTTTGGTGACATTTTGTTCACTTCATGTGGCATTATGGATGAAGTTTTTTGAGCACAAGCCTTTTGATCCACGAGC

upper sequence: LOC_Os01g07310.4 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G06890.2 (Arabidopsis thaliana), 3'ss of exon 2
ggttctaaagtgtgtg--acaatactaggtaacgtaaaaagttagtacataaatagacgtgtttcctgtccaaattactcaacttcggtctgtgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACGTGGCATTATGTATGAAGCTCTTTGAGCACAAACCTTTTGATGCAAGGAC
  || | | || ||||   | |||  || |    |   |  ||| | ||    |   |   |   || ||     |        |   | ||| | |  |||| |||||||||||||| ||||||||  | || |||||||| || ||||| ||||||||||| |||||| | || || ||||| ||||||||| || |  |
cattttgatgtctgtgttgccataacagcttttatgtcatctta-tgcaattttgatctcataagctatctgttcttactcttgttattttgtatgt-acagCGACTACTTTGACAAGTTGGCATCTTTTGGTCACATTTTGTTCCCTTCATGTGGCATTATGGATGAAGATGTTCGAACACAAGCCTTTTGATCCACGAGC

upper sequence: LOC_Os01g07310.4 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g07960.t01 (Vitis vinifera), 3'ss of exon 3
ggttctaaagtgtgtgacaatactaggtaacgtaaaaagttag-tacataaatagacgtgtttcctgtccaaattactcaact-tcggtctgtgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACGTGGCATTATGTATGAAGCTCTTTGAGCACAAACCTTTTGATGCAAGGAC
 ||   ||  | |    || |  ||  |    |        || | | |   ||     || |   || |  |||  | ||||  |   ||||   |||||||||| ||||| || ||||||||||| || || |||||||| |||||||| |||||| |||| |||||  | ||||||||||| |||||||| || ||  |
agtgaaaacttttcctccattcatatatttgctcttttcacagctgctttgttaatttagtcttgagttctcatt--ttaactacccaactgtcgattgcagCCACAACTTTAACTAGCTGGCATCTTCTGGTCACATTTTGTTCTCTTCATGTGGCACTATGGATGAAATTATTTGAGCACAAGCCTTTTGACGCTAGAGC

upper sequence: LOC_Os01g07310.4 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0067g02970.t01 (Vitis vinifera), 3'ss of exon 3
ggttctaaagtgtgtgacaatactaggtaacgtaaaaagttagtacataaatagacgtgtttcctgtccaaattactcaacttcggtctgtgttt-tgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACGTGGCATTATGTATGAAGCTCTTTGAGCACAAACCTTTTGATGCAAGGAC
| |  ||    ||   | |  ||||  ||   | |     || |     || |   |  | | ||      |||| ||  ||    || || ||| | |||| ||||| ||||||||||||||||| || || || || || |||||||| |||||  |||| |||||  | ||||| |||||||| ||||||||||   |
gctattaggcggtaacaaagcactaactataatgattgtatactttgataagatttgcttctacttgtggcatta-tcttctgtcatccgtctttgtacagCTACTACATTGACAAGCTGGCATCTTCTGGTCACTTTCTGTTCTCTTCATGTGGCTCTATGGATGAAATTGTTTGAACACAAACCATTTGATGCAAAAGC

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|29629268|gb|CB634279.1|CB634279
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
EST: gi|88404615|gb|CI581051.1|CI581051
EST:     CATGGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGTTTCCACTTCG                         CCACTACTTTGACAAGCTGGGATCTCCT-GTTA
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTA
EST: gi|88404240|gb|CI575728.1|CI575728
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCAGG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
EST: gi|58588563|gb|CF986871.1|CF986871
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
EST: gi|88389475|gb|CI600644.1|CI600644
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         ACACTACTTTGACAAGCTGGCATCTCCTC
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTC
EST: gi|88407697|gb|CI607831.1|CI607831
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTG
EST: gi|58657641|gb|CK046321.1|CK046321
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
EST: gi|88425263|gb|CI564780.1|CI564780
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
EST: gi|8857939|gb|AU095257.1|AU095257
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGGACAAGCTGGGCATCTCCTCGTTACATTTTGCTCTCTTCA
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTG-ACAAGCTGG-CATCTCCTCGTTACATTTTGCTCTCTTCA
EST: gi|88362325|gb|CI608716.1|CI608716
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGGTCTCTTCAGG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
EST: gi|88423736|gb|CI617088.1|CI617088
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAG
EST: gi|88423801|gb|CI609832.1|CI609832
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
EST: gi|3061098|gb|C91730.1|C91730
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         C-ACTACTTTGACAAGCTGGCATCTCCTCGT
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGT
EST: gi|88406984|gb|CI578512.1|CI578512
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCATTACTTTGACAAGCT
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCT
EST: gi|88426166|gb|CI574049.1|CI574049
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTC
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTC
EST: gi|58606825|gb|CK034858.1|CK034858
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
EST: gi|88312159|gb|CI582497.1|CI582497
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCA
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCA
EST: gi|86876961|gb|CI309749.1|CI309749
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
EST: gi|86850723|gb|CI309535.1|CI309535
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
EST: gi|44678003|gb|CR291437.1|CR291437
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
EST: gi|88401466|gb|CI586022.1|CI586022
EST:     -ATTGTCATCTGCAACAAGGCCCTCATGAGCTCC-TCGGCTTCAACTTCG                         CCACTACTTTGATAAGCTGGCATCT
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCT
EST: gi|88735366|gb|CI758874.1|CI758874
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTAATTTGACAAGCTGGGATTTCCTCGTTACA
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACA
EST: gi|58656550|gb|CK045230.1|CK045230
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
EST: gi|58586232|gb|CF984540.1|CF984540
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
EST: gi|58593927|gb|CF992235.1|CF992235
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACG
EST: gi|702015|gb|D48306.1|D48306
EST:     CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCG                         CCACTACTTTGACAAGCTGGCATCTCCTCGTTACAATTTTGCTCTCTTCAC
genomic: CATTGTCATCTGCAACAAGGCCCTCATGAGCTCCCTCGGCTTCAACTTCGgtatgagatc ... tgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACA-TTTTGCTCTCTTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataaatagacgtgtttcctgtccaaattactcaacttcggtctgtgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACGTGGCATTATGTATGAAGCTCTTTGAGCACAAACCTTTTGATGCAAGGAC
                        aaattact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttctaaagtgtgtgacaatactaggtaacgtaaaaagttagtacataaatagacgtgtttcctgtccaaattactcaacttcggtctgtgttttgcagCCACTACTTTGACAAGCTGGCATCTCCTCGTTACATTTTGCTCTCTTCACGTGGCATTATGTATGAAGCTCTTTGAGCACAAACCTTTTGATGCAAGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - -gtaaaaag
- - - - - - - - - - - - - - - - - - - - - - acataaa