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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatggtcaagtgggtatcgttgtgttctccttgttagcaatttgtgatctaatcttgtttctgcctaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAACACACACCTTGCATCAAACACATACCTTGTTGGCCATTCAGTGACTCTTG

Basic information

species Oryza sativa
transcript LOC_Os02g12800.5
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 6
gtaagtatggtcaagtgggtatcgttgtgttctccttgttagca-atttgtgatctaatcttgtt-tctgcctaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAACACACACCTTGCATCAAACACATACCTTGTTGGCCATTCAGTGACTCTTG
||| |||| | || ||||||| |  |   |  | ||   ||||    ||||  ||| || || |  | |||  ||||||  || ||| |||| |||||||||||||||||| |||| ||| |||| ||||| || |||||||||||||||| ||||||||| ||||||||||| ||||
gtatgtattgccatgtgggtagcact---tctttctcaatagcttgattgtagtctcatattctcatttgctcaacagACAGAAGAATCAGCCATTGCTGCTTTGAAGAGAGCATTCGGTTCCCTGAACACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACACTTG

upper sequence: LOC_Os02g12800.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G320497_T01 (Zea mays), 3'ss of exon 6
gtaagtatggtcaagtgggtatcgttgtgttctccttgttagca-atttgtgatctaatcttgtt-tctgcctaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAACACACACCTTGCATCAAACACATACCTTGTTGGCCATTCAGTGACTCTTG
||| ||||  ||| ||||  | |  |   | || ||   ||||    ||||  ||| || || |  | |||| |||||   || ||| || |||||||||| ||||||||| |||||||| | || | ||| || |||||||||||||||| ||||||||| |||||||||||||| |
gtatgtattttcatgtggccaacact---tccttctcaatagcttgattgtagtcttatattctcatttgcccaacagGTAGAAGAATCAACTATTGCTGCCTTGAAGAGAGCATTGGGTTCTCTGAGCACCCATCTTGCATCAAACACATTCCTTGTTGGGCATTCAGTGACTCTCG
















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|14192412|gb|AU184623.1|AU184623
EST:     AATGGCTCTTCCCACGTCTTGGATTTGCTCCTTATGTTGCTGTC                         AGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: AATGGCTCTTCCCACGTCTTGGATTTGCTCCTTATGTTGCTGTCgtaagtatgg ... tgcctaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
EST: gi|58653541|gb|CK042221.1|CK042221
EST:     CTGGAAAATGGCTCTTCCCACGGCTTGGATTTGCTCCTTATGTTGCTGTC                         AGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: CTGGAAAATGGCTCTTCCCACGTCTTGGATTTGCTCCTTATGTTGCTGTCgtaagtatgg ... tgcctaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
EST: gi|58691659|gb|CK080346.1|CK080346
EST:     CTGGAAAATGGCTCTTCCCACGGCTTGGATTTGCTCCTTATGTTGCTGTC                         AGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC
genomic: CTGGAAAATGGCTCTTCCCACGTCTTGGATTTGCTCCTTATGTTGCTGTCgtaagtatgg ... tgcctaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgttgtgttctccttgttagcaatttgtgatctaatcttgtttctgcctaacagAGTGAGGAAGCAGCTATTGCTGCTTTGAAGAGATCATTGGGTGCCCTCAACACACACCTTGCATCAAACACATACCTTGTTGGCCATTCAGTGACTCTTG
                              atctaat  putative branch site (score: 3)
                                    tcttgtttctgcct  CT-rich tract
                      aatttgt  TA-rich tract