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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattacattctatgcatctgtgttacacactaaattaccaatgaccttcaccactccttcaatggatcatttccagcatccatctatcagttcaccttttgactttacatctttatgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG

Basic information

species Oryza sativa
transcript LOC_Os09g28570.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G147191_T02 (Zea mays), 3'ss of exon 10
gtattacattctatgcatctgtgttacacactaaattacc-aatgaccttcaccact------------ccttcaatggatca--tttccagcat--------ccatctatcagttc-accttttgactttacatctttatgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG
|| || |||| | |||   | | |  ||||  || ||||| | |  | |    |  |             || ||    || |  |||  |  ||            || ||||| |    ||||  ||||   | |||     | |||||||||||||| ||||||||||| |||||||||||||| || ||||| ||||| ||| | ||||||||| ||||||| ||||||   ||||| |||
gtcttccattttgtgcccttctatcgcacaacaagttacctagtagcttctgtcgttgaaatgagatcatctgcagcatattaaatttgaaatatagttatgcttgcctgtcagtactggtttttatctttgttttttttctcgtgaagGTTCCAGCCAAACATCTTCTTCCAGTGCCAAGACCAGACCCTGAGGTTGTTGCAATGTTGACATCAGGACTGACTGCATCAATTAGTCTTGAAAAG

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G368058_T01 (Zea mays), 3'ss of exon 5
gtattacattctatgcatctgtgttacacactaaattaccaatgaccttcaccactccttcaatggatcatttccagcatccatctatcagttcaccttttgactttacatctttatgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG
                  ||  ||  || |  | |||  |  | ||||    || |      |   || |||||   ||   |  |||   ||  | || |      | |||||| ||||  ||| || |||||||   |||| |||| |||||||||||||| |||||||| ||||||||||||||||||||||||||||| || || || ||||| |||
----------------tcctccgt--caaatgagattttctctaacctcttgcattttgggcacc-attatttctgacaataacatatttttttgctttat------atatctttctgatgtaagATTTCAGCCAAAAGTCTTATTCCAGTGCCAAGACCAGACCCAGAGGTGGTTGCTATGCTAACATCAGGATTGACTGCATCCATCGCTCTTGAAAAG

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA02G15070.1 (Glycine max), 3'ss of exon 10
-------------------------------------------------------gtattaca--ttctatgcatc---tgtgttacacactaaattaccaatgaccttcaccactccttcaatggatcatttccagcatccatctatcagttcaccttttgactttacatcttta-tgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG
                                                        ||||  |  ||| ||| | |   | | |   | || |  |      | |  |       ||    ||||   |  |      ||  || ||| |  | |  | ||||   |   |  ||| |    | || ||||  | || |||  |||||||||||| ||||||||||| || || ||||| ||||| ||||| ||||||||||| |||||||| || || |||
gtgggcagtgcttaagataatgttttatatttttcctttcatattaatgacttaattattggagtttccatgtaccacttatttagaaaaccatgtgtttggttat-taagttgatctgataatgatactgtgatgatatttat-tatgatgtaagttattgaagctgtcttgttacttgggatagATTCCTTCAAAACATGCTCTTCCGGTGCCTAGACCAGATCCTGAAGTTGTTGCCATGCTTACATCGGGATTGACTGCCTCAATTGCTCTAGAAAAG

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G49670.1 (Arabidopsis thaliana), 3'ss of exon 10
gtattacattctatgcatctgtgttacacactaaattaccaatgaccttcaccactccttcaatggatcatttccagcatccatctatcagttcaccttttgactttacatctttatgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG
                   | ||  |   ||||||  |   |||| |  ||          | | ||   ||| ||           |||||  | | | |||   |   | |||  |||| | |||  |  | |||||| ||||||| || ||||||||||||||||| || ||||| ||||| || || ||||| ||||| | ||| |||||||| |||
------------------gtatgagaactactaaaccat--atgagcaaca----------agttgacatttttcaaggct------tcagtg-atcatgtgaacctgtctgttttggattta-gGTATCTTCTAAGCATGTTCTTCCTGTTCCAAGACCAGATCCAGAAGTTGTTGCCATGCTTACCTCGGGATTAACTGCATTAATCGCCCTTGAAAAG

upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv03s0063g00610.t01 (Vitis vinifera), 3'ss of exon 10
-----------------------------------------------gtattacattctatgcatctgtgttacacactaaattaccaatgaccttcaccactccttcaatggatcatttccagcatccatctatcagttcacctt--ttgactttacatctttatgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG
                                                 ||||  || | |   | |   ||  |     | ||    || |  ||    | |  || | |     ||    |   |  ||   | | ||   |    |||||      | |||   ||   |||||||  |||||||  | ||||| ||| |||||||||||||||| || ||||| |||||||| |||||| | || || ||||||||  | || |||
gtatactaccttaatatttttgcttttaatgttctacagggttggtgtcattattttgtttattttttaattcaattgctacttgatcataat-tttgttaataattaagttacctatcaaaaatgttaataattaaatttgtcggagttgaccccttttttttgc-atgttagGTTCCTTCCAAGCACATCCTTCCCGTGGCAAGACCAGATCCAGAAGTTGTTGCGATGCTAACCTCAGGACTTACAGCATCAATTGCTTTAGAAAAG

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|58684560|gb|CK073247.1|CK073247
EST:     CTTATGACTTTTGGGG-CTATTCTGAA-TTACTCAG                         GTTCCAGCCAAGCATCTTCTTCCGGTG-CAAGAGCAGATCCAGAGGTCGTT
genomic: CTTATGATTTTTGGGGCCTATTCTGAATTTACTCAGgtattacatt ... atgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTT
EST: gi|88405965|gb|CI591360.1|CI591360
EST:     CAGTCCTGTAGCCCTTATGATTTTTGGGGCCCTATTCTGAATTTACTCAG                         GTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATC-AGAGGTCGTT
genomic: CAGTCCTGTAGCCCTTATGATTTTTGGGGCC-TATTCTGAATTTACTCAGgtattacatt ... atgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccagcatccatctatcagttcaccttttgactttacatctttatgattaaagGTTCCAGCCAAGCATCTTCTTCCGGTGCCAAGACCAGATCCAGAGGTCGTTGCTATGCTAACATCAGGATTGACTGCTTCAATTGCCCTTGAGAAG
                           ttttgac  putative branch site (score: 3)
                                        tctttat  putative PPT
                                       atctttatgattaaa  TA-rich tract