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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctcaagttcaatacctgctaattatttgggcattgcttgaaaatattttctcatctccatcctgctactcagaggtggtcagaaaatggttagaacatgcatattcatgaaatgtgttgccatcctcattttgatttggtttgataaaattaaggattctcacttcaactctatttctcgctttagGTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAA

Basic information

species Oryza sativa
transcript LOC_Os01g23740.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G128171_T04 (Zea mays), 3'ss of exon 2
gtatgttctcaagttcaatacctgctaattatttgggcattgcttgaaaatattttctcatctccatcctgctactcagaggtggtcagaaaatggttagaacatgcatattcatgaaatgtgttgccatcctcattttgatttggtttgataaaattaaggattctcacttcaactctatttctcgctttagGTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAA
                                                                                   | | |||||||  ||     |  |||    |||| || | ||    | | | |||||    ||||| ||||||| |   | |     |  ||     |||||   ||||||||||||| ||||||||||||||| |||||||||||||||||||||| ||||| |||||||| ||||||||||| ||||||||| |||||||||||||
-----------------------------------------------------------------------------------gataagaaaattattg----acacatggctatgacatttcttc---tgcactttttg---cggtttcataaaatcattcacttatcttaaaatctggtttctttttttagGTTGATTGTGATGAGCACAAGAGTTTGTGCAGCAAGTATGGAGTTTCCGGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G25050.1 (Glycine max), 3'ss of exon 9
gtatgttctcaagttcaatacctgctaattatttgggcattgcttgaaaatattttctcatctccatcctgctactcagaggtggtcagaaaatggttagaacatgcatattcatgaaatgtgttgccatcctcattttgatttggtttgataaaattaaggattctcacttcaactctatttctcgctttagGTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAA
                                                                                                   |        | | |||   |  | |  |  |    |||  |   |  ||| || |        |||  ||  | || | | |       | |||||||| || ||||||||||||||| |||||||||| |||||||| |||||||||||||||||||| ||||| || |||||||| || || ||||||||
---------------------------------------------------------------------------------------------------gttttattgtttccattttacctttctcagtgaggattcag---taatttcattacccattaaattgacagcttaatttt-taatgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAA

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G01750.1 (Glycine max), 3'ss of exon 2
gtatgttctcaagttcaatacctgctaattatttgggcattgcttgaaaatattttctcatctccatcctgctactcagaggtggtcagaaaatggttagaacatgcatattcatgaaat--gtgttgccatcctcattttgatttggtttgataaaattaaggattctcacttcaactctatttctcgctt----tagGTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAA
                                                                                                   |    |   | || || |  |   | || || | |||| |  |  ||   |  ||   ||||   |||       || ||  |||| |    |    |||||||| || ||||||||||||||| |||||||||| |||||||| |||||||||||||||||||| ||||| || |||||||| || || ||||||||
--------------------------------------------------------------------------------------------------tgcctgtatgtttttattatttccattttacctttctcagtgaggattcagt-aatttcattacccattaaattgacagcttaatttttaatgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAA

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G01820.1 (Glycine max), 3'ss of exon 3
gtatgttctcaagttcaatacctgctaattatttgggcattgcttgaaaatattttctcatctccatcctgctactcagaggtggtcagaaaatggttagaacatgcatattcatgaaatgtgttgccatcctcattttgatttggtttgataaaattaaggattctcacttcaactctatttctcgctttagGTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAA
                                                                           |   | ||  |       || ||       |||| |       |||  |    | | |||||     ||   |||| |||  | |   || | | |  ||             | |||||||| || |||||||| |||||| ||||||||||||||||||| |||||||||||||||||||| ||||| || |||||||| || ||  |||||||
--------------------------------------------------------------------------tttgtacgtttttgt----tgtttctttttggcatttctcaatgatgattcaataacttcattacctattaaattgacaaagctta--ctttttaatgtaa-------------tgtagGTTGACTGTGATGAGCATAAGAGTTTGTGCAGCAAGTATGGAGTCTCTGGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAAGCCAAAAA

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G24520.1 (Glycine max), 3'ss of exon 3
gtatgttctcaagttcaatacctgctaattatttgggcattgcttgaaaatattttctcatctccatcctgctactcagaggtggtcagaaaatggttagaacatgcatattcatgaaatgtgttgccatcctcattttgatttggtttgataaaattaaggattctcacttcaactctatttctcgctttagGTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAA
                                                                                                                                               |  ||| || |        |||  ||  | || | | |       | |||||||| || ||||||||||||||| |||||||||| |||||||| |||||||||||||||||||| ||||| || |||||||| || || ||||||||
----------------------------------------------------------------------------------------------------------------------------------------------gtaatttcatta---cccaaattgacagcttaatttt-taatgtaatgtagGTTGACTGTGATGAGCACAAGAGTTTGTGCAGCAAATATGGAGTCTCTGGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAA

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|88354765|gb|CI614043.1|CI614043
EST:     AAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAG                         GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGG
genomic: AAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAGgtatgttctc ... ctcgctttagGTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGG
EST: gi|58598802|gb|CK009330.1|CK009330
EST:     AAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAG                         GTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGG
genomic: AAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAGgtatgttctc ... ctcgctttagGTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttggtttgataaaattaaggattctcacttcaactctatttctcgctttagGTTGATTGCGATGAGCACAAGAGTGTGTGCAGCAAGTATGGAGTTTCTGGGTACCCAACAATTCAATGGTTCCCCAAAGGATCCCTGGAGCCCAAAAA
                         ttctcac  putative branch site (score: 2)
                                     ctctatttctcgcttt  putative PPT
        tttgataaaattaa  TA-rich tract