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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagcacttgttttcttacgctaaaaatttccagaacattgttatgttctgaatatgccatattttactttctgattttttttaccatgggtttgtcagCGTGGCTTTGATTGTATTTGGAGCATTTATCGCTGGAGCTCGAGACCTGTCGTTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA

Basic information

species Oryza sativa
transcript LOC_Os02g40030.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G020976_T01 (Zea mays), 3'ss of exon 4
--------tgtagcacttgttttcttacgctaaaaatttccagaacattgttatgttctgaatatgccatattttactttctgattttttttaccatgggtttgtcagCGTGGCTTTGATTGTATTTGGAGCATTTATCGCTGGAGCTCGAGACCTGTCGTTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA
        ||    ||    ||| ||| ||| ||  ||| |||||| |      ||||||||| |   || ||  | | || | ||  |   |||| || ||| |||| ||||||||||||||||| ||||||||| | ||||||||||||||| |||| ||||||||||||||||||||||||||||||||||||||||||||||||
ctttttcttgggatacagcatttgttatgctgaacgttttcagaactt------gttctgaatctataatgttccattatccggttgcta--accaaggttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA

upper sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G133226_T04 (Zea mays), 3'ss of exon 4
tgtagcacttgt--tttcttacgctaaaaatttccagaacattgttatgttctgaatatgccatattttactttctgattttttttaccatgggtttgtcagCGTGGCTTTGATTGTATTTGGAGCATTTATCGCTGGAGCTCGAGACCTGTCGTTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA
| | |||       ||| ||| ||| ||  ||| |||||| | ||  |||||||||| |    | ||  ||| |||| || ||   || | || ||| |||| ||||||||||||||||| ||||||||  | ||||||||||||||| |||| |||||||||||||||||||||||||||||||||||||||||||| |||
ttttgcatacaacatttgttatgctgaacgttttcagaacttggtagtgttctgaatctatattgttccactatctggttgtta--actaaggttttatcagTGTGGCTTTGATTGTATTCGGAGCATTCGTTGCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACGACA

upper sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv11s0016g05710.t01 (Vitis vinifera), 3'ss of exon 4
tgtagcacttgttttcttacgctaaaaatttccag----aacattgttatgttctgaat-atgcca-tattttactttctgattttttttaccatgggtttgtcagCGTGGCTTTGATTGTATTTGGAGCATTTATCGCTGGAGCTCGAGACCTGTCGTTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA
  |   |||  |||  |     |  || |||  ||    | |||  |||  |  || || |||    || ||| ||   ||    |||  |  ||   ||   ||| || |   | ||  || |||| |||||||| ||||||||||| |||||||| |||||  |   ||| ||||||||||| |||||||| ||||||   |||
-ctcagactgatttattc---ttggaattttatagtgatagcatcattacctattgtatcatgttgctaattttctcaatggaaatttccaaaatt--ttcaccagTGTTGGGATAATCATACTTGGTGCATTTATTGCTGGAGCTCGGGACCTGTCATTTGACTCCTATGGCTATGCTATTGTTTTTGTGGCAAACATTTGTACA

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|58667565|gb|CK056251.1|CK056251
EST:     ATGGAGTATTTCTTGGCAAAACAGAAGCATACGCCACCTATAATCGGCAG                         CGTGGCTTTGATCGTATTTGGAGCATTTATCGCTGGAG
genomic: ATGGAGTATTTCTTGGCAAAACAGAAGCATACGCCACCTATAATCGGCAGgtacatgtct ... ggtttgtcagCGTGGCTTTGATTGTATTTGGAGCATTTATCGCTGGAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttctgaatatgccatattttactttctgattttttttaccatgggtttgtcagCGTGGCTTTGATTGTATTTGGAGCATTTATCGCTGGAGCTCGAGACCTGTCGTTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA
                         ttctgat  putative branch site (score: 3)
               atattttactttctga  TA-rich tract