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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaccatgagaacttgtttgatatggcattattatattgtttgatatgcattatgctaataataagatgacatccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC

Basic information

species Oryza sativa
transcript LOC_Os04g23890.4
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.3 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G032351_T01 (Zea mays), 3'ss of exon 18
aaccatgagaacttgtttgatatggcattattatattgtttgatat-gcatt--atgctaataataagat-gacatccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC
    | |  | |    |||  |   | || | |     | | |||| |||||  | | | ||| |    | ||  | |    | | |   | |||||| |||||||||||| |||||||| ||| ||||||| ||||||||||| ||||||||||||||||||| ||||||| |||| || |||||||||||||||||||||||
----aagtaatcccaattgcgaattccttgtcaagagatcttatatagcattccaggttgatactgtctttgaggttctcacacccttcttccccatgatatagGAATTCTCTTGTATGAAATGTTGTATGGACGTACACCTTTTCGAGGAAAGAACAGGAAAAGGACATTTCATAATATCCTGCACAAAGACCTTACATTTCC

upper sequence: LOC_Os04g23890.3 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA08G33520.1 (Glycine max), 3'ss of exon 2
-aaccatgagaacttgtttgatatggcattattatattgtttgatatgcattatgctaataataagatgac--atccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC
           |||  | |  |||   ||||    ||||||||||   ||     ||| |  | | ||     || | | |  | |  ||   |    || ||| ||  | |||||||||||||| ||||| |||||||| ||| |||||||||| ||  | ||||||||||  || ||  | ||||| || ||||| |||||
tcttttctcacactcctcttttatta-attaagtcattgtttgattatcacatccctatttttgacattctcgattctgtttcctt--atcttctgaataaagGTATCTTGTTGTATGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAATATTTTACACAAGGATCTTACCTTTCC

upper sequence: LOC_Os04g23890.3 (Oryza sativa), 3'ss of exon 19
lower sequence: GLYMA16G19560.1 (Glycine max), 3'ss of exon 21
-aaccatgagaacttgtttgatatggcattattatattgtttgatatgcattatgctaataataagatg-acatccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC
 ||   | |  |||| ||| |      ||||    || |||||||   ||     | |    | | ||  ||       |  | | |  | |     |||||| ||  | |||||||||||||| ||||| |||||||| ||| |||||||||| ||  | ||||||||||  |||||  | ||||| || ||||| |||||
aaatagttattactt-tttcactcattattaagtcatcgtttgattatcacagcccgatgtttgacatttacgatttcgtttccttatcttctg-aatatagGTATCTTGTTGTATGAGATGCTCTATGGTCGTACACCATTCAGAGGAAAGAATAGACAGAAGACATTTTCCAACATCTTACACAAGGATCTTACCTTTCC

upper sequence: LOC_Os04g23890.3 (Oryza sativa), 3'ss of exon 19
lower sequence: AT5G58140.2 (Arabidopsis thaliana), 3'ss of exon 20
aaccatgagaacttgtttgatatggcattat---tatattgtttgatatgcattatgctaataataagatgacatccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC
              || | || || || |||   ||  || |||      ||   || || ||||| | | |  |||   ||   |   ||    || | |||| ||  | |||||||||||||| ||||| || ||||||||| | || ||||| ||| |||||||||||   |||||  |||||||||| || || || ||
--------------gtataatctgccactatctttaccttattttgatcacaaactgttattaatatgctcatctcctttta-tgtgtgtt----tgttgtagGTATCTTGTTGTATGAGATGCTTTATGGTCGCACACCTTTCAGGGGTAAGAATAGGCAAAAGACATTTGCCAACATCTTGCACAAAGATCTCACTTTCCC

upper sequence: LOC_Os04g23890.3 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv03s0038g04210.t01 (Vitis vinifera), 3'ss of exon 19
aaccatgagaacttgtttgatatg---gcattattatattgtttgatatgcattatgctaataataagatgacatccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC
|||| |       || || || ||   ||   |  ||||| |     || | |   |     | |   ||| | ||         |   |        |  ||| ||| |  ||||||||||||| ||||| ||||| |||||| |||||||||| ||| | ||||||||||  |||||  |||||||||| || || |||||
aacctt---tttctgcttaatttgcttgctggaggatattctgcctaattcttctagtccccattttcatgccttcatttgtttgttcctgtttgattttcagGGATTTTTCTGTATGAGATGCTTTATGGCCGTACTCCTTTCAGAGGAAAGAATAGGCAGAAGACATTTTCCAACATCTTGCACAAAGATCTGACTTTTCC

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|29613844|gb|CB618857.1|CB618857
EST:     ATACAAGTGCAATCGATTGGTGGGCTCTGG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: ATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|88578420|gb|CI687351.1|CI687351
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
EST: gi|33381050|gb|CF196393.1|CF196393
EST:     GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG                         GAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA
genomic: GGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCGgtaagcaata ... catgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcattatgctaataataagatgacatccagctaacatcaattcccatgctatagGAATTCTATTGTATGAGATGCTGTATGGGCGTACACCTTTCCGAGGAAAGAACAGGAAAAAGACATTTTATAACATACTGCACAAAGACCTTACATTTCC
                             agctaac  putative branch site (score: 2)
                                         ttcccat  putative PPT
     tatgctaataataa  TA-rich tract