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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtaggatggttagtgacagggataatgcgaggggctgcaataaacgacttattttcaacattgacaaaagagaacttgaaaattttacctgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCC

Basic information

species Oryza sativa
transcript LOC_Os02g47600.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47600.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G046587_T03 (Zea mays), 3'ss of exon 1
-----agtaggatggttagtgacagggataatgcgaggggctgcaataaacgacttat-tttcaacattgacaaaagagaacttgaaaattttacctgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCC
       ||| |    ||    |  || | | | | |||  |||     ||  ||| | |||  || ||||||  ||  ||       || |||| |||  | ||||| || ||||||||||| || ||||||||||||||||| |||||||| ||||||||||||||||| ||||||||    |||||| |||| |||||| | |
tgaatgttagtaacactaacacctagggttaag-gtgggcttgcttgctacatcttgtcttttcactttgacagtaggtaatc---ggatattacttgt--tacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATAC

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G07530.1 (Glycine max), 3'ss of exon 4
-----------------------------------------------------------------agtaggatggttagtgacagggataatgcgaggggctgcaataaacgacttattttcaacattgacaaaagag-aact---tgaaaattttacctgt------gtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCC
                                                                  | | ||   |   | |   ||||| |         | | ||     | ||  | ||   | |||   |  |  ||||   | |  | | | |   |         | ||||||||||| ||||||||||||| || || |||||||||||||||||||| || ||| | ||  ||||||| ||| |||| || |||||||| || || |
gtgtggttgccattttcttgcattcctcttcttcatttccttatgcttgatgtatttgcaaaatatgaaagactttcttttaataggatagtattctcatttaccatttcgaagtttatgtctgtactgaagcataactaactcactaacgaatgtgctgatcaacccaacttagGTTGATCGTATTCTTTACTCATCAGTAGTCTACCCACACAACTATGGTTTTATCCCAAGAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTC

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G37790.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------------------------agtaggatggttagtgacagggataatgcgaggggctgcaataaacgacttattttcaacattgacaaaagag-aactt------gaaaattttacctg---tgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCC
                                                                                     | ||||   || | |  ||   |  ||         |       |   ||   | ||     |||   |  |  ||||       |||  || |            | ||||||||||| ||||||||||||| ||||| |||||||||||||||||||| || ||| | ||  ||||||| ||| |||| || |||||||| || || |
gtgtcgtttccattttctttcttgcactcctcttcttccattccatatgcttaatgtattagcaaaatgtgaaagactttcttttaatagggcagt-attctcatttaccatttccaaatttatttctcattgctacctgtctgtggtgaagcataactaactcactaacgaatgttctgatcaacccaacttagGTTGATCGTATTCTTTACTCATCAGTTGTCTACCCACACAACTATGGTTTTATCCCAAGAACCATTTGTGAAGACAGTGATCCTATGGACGTGCTGGTTC

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0023g02050.t01 (Vitis vinifera), 3'ss of exon 3
agtaggatggttagtgacagggataatgcgaggggctgcaataaacgacttattttcaacattgacaaaagaga-acttgaaaattttacctgtgttt---cagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCC
       | | |  |      | ||  | |  |       |||   || || | |      |  | | |  ||| |  | || | |  |  | |        ||||||||||||||||||||||||| |||||||| ||||| |||||||||||||| || || ||  | ||||| ||| | || || ||||| |||||  | |
----tttttgcttatattgctgttatagtgttgctagattatatctgatttgtgtatgcactcaatatataagatagctaaagaatggagttctccaaaaatagGTTGATCGTGTTCTTTACTCATCAGTTGTTTATCCACATAACTATGGTTTCATCCCTCGAACCATCTGTGAAGACAGCGATCCTATGGATGTCCTGATTC

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S552_1V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------agtaggatggttagtgacaggg----ataatgcgaggggctgcaataaacgacttattttcaacattgacaaaagagaacttgaaaattttacctgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCC
             | ||  | ||  |||  |||     ||||||  |  |  |  ||  | |   | |||  | |  | |           ||   ||  |    ||   | ||||| |||||| | || ||||| ||||| || ||||| ||||| |||||||||||||||||||| ||||| |||||||  || ||||| || || || ||| 
gtgaatgtttagattgggagatttctgaaggggtttggtaatgcatgttgacgagatgtatgctgtgtttcgaccgctcattg--------ttctgaacatcggttgctctgcagGTGGATCGTATCCTATACTCGTCTGTGGTGTACCCGCACAATTATGGTTTCATTCCACGCACCCTTTGCGAGGACGAGGATCCCATCGATGTTCTGGTCA

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
agtagg--atggttagtgacagggataatgcgagg--ggctgcaataaacgacttattttcaacattgacaaaagagaacttgaaaatttta--cctgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCC
 ||| |  || |  ||||||       |  |||    | || ||       ||    | |   | | |   ||  |   ||    ||| |||  |   | ||||||||||||||| |  | |||||||| ||||| || |||||||| ||||| ||||||||||| || ||||||||||| |  || ||||| || || |||||| 
-gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggctcaaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCA

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S315_67V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------agtaggatggttagtgacaggg----ataatgcgaggggctgcaataaacgacttattttcaacattgacaaaagagaacttgaaaattttacctgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCC
             | ||  | ||  |||  |||     ||||||  |  |  |  ||  | |   | |||  | |  | |           ||   ||  |    ||   | ||||| |||||| | || ||||| ||||| || ||||| ||||| |||||||||||||||||||| ||||| |||||||  || ||||| || || || ||| 
gtgaatgtttagattgggagatttctgaaggggtttggtaatgcatgttgacgagatgtatgctgtgtttcgaccgctcattg--------ttctgaacatcggttgctgtgcagGTGGATCGTATCCTATACTCGTCTGTGGTGTACCCGCACAATTATGGTTTCATTCCACGCACCCTTTGCGAGGACGAGGATCCCATCGATGTTCTGGTCA

upper sequence: LOC_Os02g47600.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 2
agtaggatggttagtgacagggataatgcgaggggctgcaataaacgacttattttcaacattgacaaaagagaacttgaaaattttacctgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCC
                                         | ||    ||  | |   | ||  | |      | || |   |||   |  | || ||||||||||| || ||||| || || || ||||| |||||||||||||| ||  |||||||||| || ||||| |||  ||||||  | ||||| || ||  
--------------------------------------gtgtgaatagtttgatcttttctttcgctactttccagtt-atgctttggtcgttcttccagGTTGATCGAGTCCTTTATTCCTCGGTGGTTTATCCACACAACTATGGATTTGTTCCACGCACGCTGTGTGAAGACAATGACCCGCTTGACGTTCTTGTGA

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|163926919|gb|EG715144.1|EG715144
EST:     GAGTTGGATAAGGCAACTGGTCTAATTAAG                         GTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTC
genomic: GAGTTGGATAAGGCAACTGGTCTAATTAAGgtaaagctca ... tgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTC
EST: gi|58601442|gb|CK011970.1|CK011970
EST:     GAGGCAGCAAGGTTAAGTATGAGTTGGATAAGGCAACTGGCCTAATTAAG                         GTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTC
genomic: GAGGCAGCAAGGTTAAGTATGAGTTGGATAAGGCAACTGGTCTAATTAAGgtaaagctca ... tgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTC
EST: gi|163929548|gb|EG709315.1|EG709315
EST:     GAGGCAGCAAGGTTAAGTATGAGTTGGATAAGGCAACTGGTCTA-TTAAG                         GTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTC
genomic: GAGGCAGCAAGGTTAAGTATGAGTTGGATAAGGCAACTGGTCTAATTAAGgtaaagctca ... tgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTC
EST: gi|58689221|gb|CK077908.1|CK077908
EST:     GAGGCAGCAAGGTTAAGTATGAGTTGGATAAGGCAACTGGCCTAATTAAG                         GTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTC
genomic: GAGGCAGCAAGGTTAAGTATGAGTTGGATAAGGCAACTGGTCTAATTAAGgtaaagctca ... tgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTC
EST: gi|88338355|gb|CI655544.1|CI655544
EST:     GAGGCAGCAAGGTTAAGTATGAGTTGGATAAGGCAACTGGTCTAATTAAG                         GTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTC
genomic: GAGGCAGCAAGGTTAAGTATGAGTTGGATAAGGCAACTGGTCTAATTAAGgtaaagctca ... tgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTC
EST: gi|58688425|gb|CK077112.1|CK077112
EST:     GAGGCAGCAAGGTTAAGTATGAGTTGGATAAGGCAACTGGCCTAATTAAG                         GTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTC
genomic: GAGGCAGCAAGGTTAAGTATGAGTTGGATAAGGCAACTGGTCTAATTAAGgtaaagctca ... tgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgacttattttcaacattgacaaaagagaacttgaaaattttacctgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCC
              cattgac  putative branch site (score: 3)
                                      ttttacct  putative PPT
                            aacttgaaaatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtaggatggttagtgacagggataatgcgaggggctgcaataaacgacttattttcaacattgacaaaagagaacttgaaaattttacctgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - gggctgc
- - - - - - - - - - - - - - - - - - - -aataaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacaaaa