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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattattctttcattgtttctagtccagtagatatagcatttctttttaccatgttgtacccatcatagccaattatcctgacttagtttgcatgttaccagTGAAAACAAAGGGACCTTGGATGAGTCAGACCGTTTCCTCATGAACCCAGCAGATTTTGTGGGCGAGGTTTTTGGAAATTTATCTTCGTTCAGTCATATT

Basic information

species Oryza sativa
transcript LOC_Os01g39810.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39810.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G164175_T02 (Zea mays), 3'ss of exon 9
gtgattattct-ttcattgtttctagtccagtagatatagcatttctttttaccatgttgtaccc-atcatagccaattatcctgacttagtttgcatgttaccagTGAAAACAAAGGGACCTTGGATGAGTCAGACCGTTTCCTCATGAACCCAGCAGATTTTGTGGGCGAGGTTTTTGGAAATTTATCTTCGTTCAGTCATATT
||| ||||| | ||  || |||   | | |  | |  || | |||| | |    |  |||| |   |  | |  |     | |||||    | | | ||    |||||| | |||||||||||||||||||||||| |||||||| |  |  ||| | || ||||| |||||||||||||||||||||||| | |||||||| |||
gtggttattttctttgttttttaatgacaaaaatagttaacctttcatatctatac-ttgtgcttgaatacatacgtccctgctgacgcgttctac-tgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGAGGTTTTTGGAAATTTATCTGCATTCAGTCACATT

upper sequence: LOC_Os01g39810.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G000937_T02 (Zea mays), 3'ss of exon 9
gtgattattctttcattgtttctagtccagtagatatagcatttctttttaccatg-ttgtaccc-atcatagccaattatcctgacttagtttgcatgttaccagTGAAAACAAAGGGACCTTGGATGAGTCAGACCGTTTCCTCATGAACCCAGCAGATTTTGTGGGCGAGGTTTTTGGAAATTTATCTTCGTTCAGTCATATT
||| ||||| | |  |  ||| || |  |  | |||    |  | |  |  | ||  |||| |   |  | |        | ||||||   | | | ||    |||||| | |||||||||||||||||||||||| |||||||| |  |  ||| | || ||||| ||||| |||||||||||||||||| | |||||||| |||
gtggttattttatt-tgttttttaatgaaaaaaatagttaacctttcatatctatacttgtgcttgaatacatatgtccctgctgactcgttctac-tgcactcagTGATAGCAAAGGGACCTTGGATGAGTCAGATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGATGTTTTTGGAAATTTATCTGCATTCAGTCACATT

upper sequence: LOC_Os01g39810.4 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G103473_T01 (Zea mays), 3'ss of exon 2
gtgattattctttcattgtttctagtccagtagatatagcatttctttttaccatg-ttgtaccc-atcatagccaattatcctgacttagtttgcatgttaccagTGAAAACAAAGGGACCTTGGATGAGTCAGACCGTTTCCTCATGAACCCAGCAGATTTTGTGGGCGAGGTTTTTGGAAATTTATCTTCGTTCAGTCATATT
||| ||||| | |  |  ||| || |  |  | |||    |  | |  |  | ||  |||| |   |  | |        | ||||||   | | | ||    |||||| |||||||||||||||||||||||| | |||||||| |  |  ||| | || ||||| ||||| |||||||||||||||||| | |||||||| |||
gtggttattttatt-tgttttttaatgaaaaaaatagttaacctttcatatctatacttgtgcttgaatacatatgtccctgctgactcgttctac-tgcactcagTGATAACAAAGGGACCTTGGATGAGTCACATCGTTTCCTTACAAGTCCATCTGAGTTTGTCGGCGATGTTTTTGGAAATTTATCTGCATTCAGTCACATT

upper sequence: LOC_Os01g39810.4 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv11s0037g01100.t01 (Vitis vinifera), 3'ss of exon 9
---------gtgattattctttcattgtttctagtccagtagatatagcatttctttttaccatgttgtacccatcatagccaattatcctgacttagtttgcatg-ttaccagTGAAAACAAAGGGACCTTGGATGAGTCAGACCGTTTCCTCATGAACCCAGCAGATTTTGTGGGCGAGGTTTTTGGAAATTTATCTTCGTTCAGTCATATT
               ||| | |        ||  ||  || |   || |||||  |       | ||  |  || |||  | |||| |  |   || |   |  || ||||||||||| | ||||| ||| |||||||||||||||||||| | ||| | |||||   |||||     ||  ||     |||||  |||      ||||| |||
gttttaacttcatccattttgtgggaaaaccttatcttgttgtgctatcatttactaaagatttatttgatgcaacatt-ctaattttggt--tttggggggtttggttaccagTGAAGAGAAAGGAACCCTGGATGAGTCAGACCGTTTCATGATGGATCCAGCTAGTTTTGCATCAGAATTTGCAATAAATTGGTCTCTACCTAGTCACATT

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|86427881|gb|CI072978.1|CI072978
EST:     TCTACATTACATTACAACCTACCTATGCGCTTTTTGGACTGTACTCCTAG                         TGAAAACAAAGGGACCTTGGATGAGTCAGACCGTTTCCTCATGAACCCAGC
genomic: TCTACATTACATTACAACCTACCTATGCGCTTTTTGGACTGTACTCCTAGgtgattattc ... atgttaccagTGAAAACAAAGGGACCTTGGATGAGTCAGACCGTTTCCTCATGAACCCAGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccatgttgtacccatcatagccaattatcctgacttagtttgcatgttaccagTGAAAACAAAGGGACCTTGGATGAGTCAGACCGTTTCCTCATGAACCCAGCAGATTTTGTGGGCGAGGTTTTTGGAAATTTATCTTCGTTCAGTCATATT
                             tcctgac  putative branch site (score: 2)
                        aattat  TA-rich tract