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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaatccccaaccccaattaacatccgatcatctcatttcatgtgcctaacttaacttctttttgttctgaattctagccttgattaattaattaatcctgttcttgcaatgaatccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCT

Basic information

species Oryza sativa
transcript LOC_Os02g08440.4
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08440.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G11960.1 (Glycine max), 3'ss of exon 3
gtacgaatccccaaccccaattaacat--ccgatcatctcatttcat----gtgcctaactt---aacttctttttgttctgaattctagccttgattaattaattaatcctgttcttgcaatgaatccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCT
     | | || ||      ||    |  || |  | ||  | | ||    ||| |||  ||   ||  |   ||   ||  | | ||| |   || |  | ||||  |  | || ||      |||  | | | ||| ||   || || || ||||||||||| ||||||||||||||||| | ||| ||||| |  || || || |||||||| ||||| | ||| ||    |
--gtaagttcctaaaatatgttgttgtttcctagtaacttctattatagttgtgtctatattgggaagcttaattaactccaagtactaactgggaatcctgaatttgtttttttttttggtataattaaagTATGTGATG---GACGGATATCAATGGAGGAAATATGGTCAGAAGGTCACTAGGGATAACCCTTCTCCTAGGGCTTACTTCAGGTGCTCCTCTGCCCCAAGTT

upper sequence: LOC_Os02g08440.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G33890.1 (Glycine max), 3'ss of exon 2
--------gtacgaatccccaaccccaattaacatccgatcatctcatttcatgtgcctaacttaacttctttttg-ttctgaattctagccttgattaattaattaatcctgttcttgcaatgaatccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCT
         ||  | |             | | | |   |  | |  |||  |||   ||   | |  | |  |    ||  | | ||| |   || |  | ||||  |  | ||  |    || | | |   ||   ||||  || || || ||||||||||| ||||||||||| ||||| | ||| ||||| |  || ||||| |||||||| ||||| ||||| ||   ||
gtaagttcctaaaatttattgttgtttcctgataacttgtattatagttttgtgtatatattgtgaggtttaatcaactccaagtactatctgggaatcctgaatttgttttttttattttgtgtaacta--aagTATGTGATGGACGGATATCAATGGAGGAAATATGGTCAGAAAGTCACTAGGGATAACCCTTCTCCTAGAGCTTACTTCAGGTGCTCCTTTGCCCCAAGCT

upper sequence: LOC_Os02g08440.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G02630.1 (Glycine max), 3'ss of exon 3
gtacgaatccccaaccccaattaacatccgatcatctcatttcatgtgcctaac--ttaacttctttttgttctgaattctagccttgattaattaattaatcctgttcttgcaatgaatccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCT
                             |    |||| || |  || |  ||   ||   |  |     |     |  |||     |  ||| |  || |     || |     ||  |   | ||| | || |||||||| |||||||||||||| ||||| || ||||| ||||  || ||||| || || ||||| || ||||  ||||| ||||||||   ||
-----------------------------gtaagtctctttactagtactcaatctttggttcttggacatggcatagactatataggggtaagtgtttgacagatttttcattgtgtgtggtttcagATTGTTAAAGATGGATACCAATGGAGGAAATATGGGCAAAAGGTGACCAGAGATAACCCTTGTCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCTAGCT

upper sequence: LOC_Os02g08440.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G44730.1 (Glycine max), 3'ss of exon 3
gtacgaatccccaaccccaattaacatccgatcatctcatttcatgtgcctaacttaacttctttttgttctgaattctagccttgattaattaattaatcctgttcttgcaatgaatccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCT
                             |      || |  ||    |  | | |||    |  ||    |   || |    | | || |     |  |    || ||    || |||||    | | ||||||||||| || ||||||||||| ||||| || ||||| |||| ||| ||||| |  |||||||| || ||||  ||||| ||||||||   ||
-----------------------------gtaagattcttaacagcaactgagcataaaaagtcattaccattg-ttgtgcattagtttgacaggct--tttcatttttttcgtgtatcca----gATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGGGATAACCCTTCTCCAAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT

upper sequence: LOC_Os02g08440.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G23380.3 (Glycine max), 3'ss of exon 3
gtacgaatccccaaccccaattaacatccgatcatctcatttcatgtgcctaacttaacttcttt----ttgttctgaattctagccttgattaattaattaatcctgttcttgcaatgaatccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCT
                             |    |||| || |  || |    |||   ||||||    | |    || |  |    | |  ||| |  || |     || |     |   |   |  || | ||||||||||| |||||||||||||| ||||| || ||||| ||||  || ||||| | ||| ||||| || ||||  ||||| ||||||||   ||
-----------------------------gtgagtctctttactagtactctcctttggttctttgacatagcatagactatttaaatagggtaagtgtttgacagatttttcattgtatgtggttttagATTGTGAAAGATGGATACCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTACCCTAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT

upper sequence: LOC_Os02g08440.4 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G80840.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacgaatccccaaccccaattaacatccgatcatctcatttcatgtgcctaacttaacttctttttgttctgaattctagccttgattaattaattaatcctgttcttgcaatgaatccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCT
                              | ||| ||||   |     | |||||    ||| | | |  | |     | | ||  || ||    |   |   || | | | |   | | |  |||| |||||||||||||| ||||||||||| ||||| ||||| || || |  ||||| || |  |||||||| ||||||| |||  | | ||||||   ||
---------------------------gtaagcat-tcatgaaaatgatcaaacttggtatctatctatctttaga---aactttattttatatggtttactgattgtagaagttgtttcttatagGTTGTGAAAGATGGGTATCAATGGAGGAAATATGGACAGAAAGTGACTAGAGACAATCCATCTCCAAGAGCTTACTTCAAATGTGCTTGTGCTCCAAGCT

upper sequence: LOC_Os02g08440.4 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv09s0018g00240.t01 (Vitis vinifera), 3'ss of exon 3
gtacgaatccccaaccccaattaacatccgatcatctcatttcatgtgcctaacttaacttctttttgttctgaattctagccttg-attaattaattaatcctgttcttgcaatgaatccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCT
                     |||  ||| |    | ||  | ||  ||   ||||   |   || |  | ||||  | | ||    | | | | ||  |||  |   || |  |   |   | ||||||||||| ||||| ||||| |||||||| ||||| || ||||||||||  ||||||||||  || ||||||||||||| |||||| ||||||||   ||
--------------------gtaa-gtccaaaacccacaaataattggc--gactttggtggattattctgtgaacaccatccggatagtgaatgatcgatcgagcaatttctttatgttt-tacagGTGGTGAAGGATGGATACCAGTGGAGGAAATATGGCCAAAAGGTCACCAGAGACAACCCCTCTCCGAGAGCCTACTTCAAATGCTCTTTTGCTCCTAGCT

upper sequence: LOC_Os02g08440.4 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0008g05760.t01 (Vitis vinifera), 3'ss of exon 3
gtacgaatccccaaccccaattaacatccgatcatctcatttcatgtgcctaacttaacttctttttgttctgaattctagcc--ttgattaattaattaatcctgttcttgcaatgaatccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCT
            |   |      | |       || |     ||  ||    |  ||   || || ||   ||| ||||   |  ||  |      |   |||||||| |     ||  |   ||||| |  |||| || || ||||||||||| |||||||| |||||||||||||  || ||||| |  || |||||||||||||  ||||| ||||| ||  |||
---------gtaagttctggcctagacatagaaatttatgaacaattggtggaagta--ctccttctgccatgatttctgatcaattagtactaagaacgatcctgttttcttcctgggtttttgcagCTTCTGAAGGACGGATACCAATGGAGAAAGTATGGGCAGAAGGTCACCAGAGATAACCCTTCTCCCAGAGCCTACTTCAAGTGCTCCTTTGCCCCAACCT

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|87035375|gb|CI189997.1|CI189997
EST:     CCATCCGACCTCAGCCTG                         GTGGTGAAAGATGGGTACCCATGGAGGAAGTATGGTCAGAAGGTCACCAAG
genomic: CCATCCGACCTCAGCCTGgtacgaatcc ... atccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAG
EST: gi|29659288|gb|CB655563.1|CB655563
EST:     CCAAGATCTCCAAGCTCTACGTCCACGCCGACCCATCCGACCTCAGCCTG                         GTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAG
genomic: CCAAGATCTCCAAGCTCTACGTCCACGCCGACCCATCCGACCTCAGCCTGgtacgaatcc ... atccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAG
EST: gi|38475576|gb|CF959709.1|CF959709
EST:     CCAAGATCTCCAAGCTCTACGTCCACGCCGACCCATCCGACCTCAGCCTG                         GTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAG
genomic: CCAAGATCTCCAAGCTCTACGTCCACGCCGACCCATCCGACCTCAGCCTGgtacgaatcc ... atccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAG
EST: gi|29664850|gb|CB661125.1|CB661125
EST:     CCAAGATCTCCAAGCTCTACGTCCACGCCGACCCATCCGACCTCAGCCTG                         GTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAG
genomic: CCAAGATCTCCAAGCTCTACGTCCACGCCGACCCATCCGACCTCAGCCTGgtacgaatcc ... atccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattctagccttgattaattaattaatcctgttcttgcaatgaatccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCT
                      aattaat  putative branch site (score: 3)
            ttgattaattaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgaatccccaaccccaattaacatccgatcatctcatttcatgtgcctaacttaacttctttttgttctgaattctagccttgattaattaattaatcctgttcttgcaatgaatccatgcagGTGGTGAAAGATGGGTACCAATGGAGGAAGTATGGTCAGAAGGTCACCAAGGACAACCCCTGCCCAAGAGCCTACTTCAGATGCTCATTTGCTCCCGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG