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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctggggacaaacagttctatatttgtctactcttgaactgttggtttggtttggttgacgttttactttttatggcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGGGAAATCTATGACCAATATGGCGAGGATGCACTCAAAGAAGGAATGGGAG

Basic information

species Oryza sativa
transcript LOC_Os02g43930.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 2
-----gtctggggacaaacagttct---atatttgtctactct-tg-aactgttggtttggtttggttgacgttttacttttt-atggcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGGGAAATCTATGACCAATATGGCGAGGATGCACTCAAAGAAGGAATGGGAG
      ||||   |||    |||||   ||||| |  || | | || || ||| ||| |  |       | ||||| |||  | |||   | | |||||||||||  || |||||||||| || ||||||| ||| || || |||||||| ||||||||||| ||||| || ||||| || || |||||||||||||
gtttgttctgtccacattt-gttctgtaatattagcttagtatgtgcaattgtaggtgttctcatcgccaggttttccttgatgatgaacttggcagTTTAAAGAGCTGTCTCAAGCTTATGATGTTCTTAGTGACCCGGAGAAGAGGGAGATCTATGACCAGTATGGAGAAGATGCCCTTAAGGAAGGAATGGGAG

upper sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv15s0021g02090.t01 (Vitis vinifera), 3'ss of exon 2
-----gtctggggacaaacagttctatatttgtctactcttgaactgt---tggtttggt----ttggttgacgttt-tactttttatggcttggt--cagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGGGAAATCTATGACCAATATGGCGAGGATGCACTCAAAGAAGGAATGGGAG
     | ||| | | |  || ||| | | ||   ||       | | |   |  | |  |    ||  || || | | || || ||||   || ||  ||||| || || ||| |||||||||| || |||||||  ||||| || || || |||||||||||||||||||| || ||||  || ||||| ||||||||||
cttatgcctgtgca-aggcaattcaaaactttcttagcaaaagagtttctctaatctattcctattttttaacttgtatagttgttatatttttgtatcagTTCAAGGAGTTGTCTCAAGCTTATGATGTTCTTAGCGATCCAGATAAAAGAGAAATCTATGACCAATATGGTGAAGATGGGCTTAAAGAGGGAATGGGAG

upper sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S17_208V6.1 (Physcomitrella patens), 3'ss of exon 1
-gtctgggg-----acaaacagttctatatttgtctactcttgaactgttggtt---tggtttggtt--gacgttttac--tttttatggcttggt-cagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGGGAAATCTATGACCAATATGGCGAGGATGCACTCAAAGAAGGAATGGGAG
   ||  ||         |   |||| || |||   |||       | |||  |   || ||| |||   | ||  ||      | | | ||   | ||||| |||||  | ||||| |||||||| ||||| | |||||| || ||| | ||||| || || || ||||| || ||||| ||||||||||||||||| |
aacctaaggcgattgtgcaatcttctgtacttggtgacttgaagggtcttgagtatgtgatttagtttaaatgtactaaggcgctgacgtctatatgcagTTCAAAGAGCTTGCTCAGGCTTACGAAGTTCTAAGTGATCCGGAGAAGCGTGAAATATACGATCAGTATGGTGAAGATGCTCTCAAAGAAGGAATGGGTG

upper sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S342_16V6.2 (Physcomitrella patens), 3'ss of exon 1
-----gtctggggacaaacagttctatatttgtctact-------cttgaactgttggtttggtttggttgacgttttactttttatggcttggt--cagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGGGAAATCTATGACCAATATGGCGAGGATGCACTCAAAGAAGGAATGGGAG
        |||   ||| |   | ||   | || |          ||||||||   | |||  ||   | || |  | |    ||   |  || |  |||||||| ||| | ||||| |||||||| ||| | | ||||||||| ||| | || || ||||| |||||||| || |||||||| |||||||||||||| |
tgtagacatggctgcaagctcgtgtactgtggtatgagagagggacttgaacttgggatttaattctctggagggctgagacgtttatgtatgcttgcagTTTAAGGAACTTGCTCAGGCTTACGAAGTTTTGAGTGATCCTGAGAAGCGTGATATATATGATCAATATGGTGAAGATGCACTTAAAGAAGGAATGGGTG

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|29673001|gb|CB669276.1|CB669276
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|58655503|gb|CK044183.1|CK044183
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|58666150|gb|CK054836.1|CK054836
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|58658345|gb|CK051083.1|CK051083
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|58601753|gb|CK012281.1|CK012281
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|58601372|gb|CK011900.1|CK011900
EST:     -TGAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|58658625|gb|CK047305.1|CK047305
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|58663897|gb|CK052583.1|CK052583
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|58604589|gb|CK015117.1|CK015117
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|58672684|gb|CK061370.1|CK061370
EST:     ACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: ACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|29627563|gb|CB632574.1|CB632574
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|218489299|gb|FG965759.1|FG965759
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|58695486|gb|CK084173.1|CK084173
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|58664824|gb|CK053510.1|CK053510
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|29619928|gb|CB624940.1|CB624940
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|58679094|gb|CK067781.1|CK067781
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCT
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCT
EST: gi|33796281|gb|CF324007.1|CF324007
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|33795773|gb|CF323756.1|CF323756
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|58659104|gb|CK047784.1|CK047784
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCT
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCT
EST: gi|58687630|gb|CK076317.1|CK076317
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|88343932|gb|CI654968.1|CI654968
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|58660176|gb|CK048856.1|CK048856
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|29683463|gb|CB679738.1|CB679738
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
EST: gi|29631437|gb|CB636446.1|CB636446
EST:     GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAG                         TTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG
genomic: GTAAAGCTGCCATTAAAAACCACCCTGATAAGGGTGGAGACCCTGAGAAGgtctggggac ... gcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttgaactgttggtttggtttggttgacgttttactttttatggcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGGGAAATCTATGACCAATATGGCGAGGATGCACTCAAAGAAGGAATGGGAG
                       ggttgac  putative branch site (score: 4)
                               ttttactttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctggggacaaacagttctatatttgtctactcttgaactgttggtttggtttggttgacgttttactttttatggcttggtcagTTTAAAGAATTGGCTCAAGCTTACGAGGTTCTTAATGATCCTGAAAAGAGGGAAATCTATGACCAATATGGCGAGGATGCACTCAAAGAAGGAATGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA