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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagtgttacacacaattggcatgtgatttctcattgcctggccattaacttgtacctgtaattgaacattattgacaagtgtttgtactatattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGGATTCAATCTCTGCTCCCCCTGCTTTTGCAGCAGCAGAGTTCCCAGCTAG

Basic information

species Oryza sativa
transcript LOC_Os08g44820.4
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44820.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G125777_T01 (Zea mays), 3'ss of exon 4
cagtgttacacacaattggcatgtgatttctcattgcctggccattaacttgtacctgtaattgaacattattgacaag-tgtttgtactatattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGGATTCAATCTCTGCTCCCCCTGCTTTTGCAGCAGCAGAGTTCCCAGCTAG---
   ||   ||| ||  | | |     |  | |  || ||| || ||  |||  |||||||| |  |||||  ||||||| | |||||  | | ||| ||||||   ||| | |||||||||   || || ||| | ||||||| |||  ||||||| |||||||||||||| |||||||||| ||   |||||||| |||    
-catgacccactcatgtaggagcatttggcactgtgtctgtcctttttcttacacctgtaaatagacattgatgacaaggtttttgtgttgtgttcaacagATGGTCAGGCTAAGAGTAGTACTATTGGAAAGGGATTTGTAAGGATTTTGGATTCGATCTCTGCTCCCCCAGCTTTTGCAGGAG---AGTTCCCATCTAACCA
















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|313080704|gb|HO213501.1|HO213501
EST:     TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAG                         ATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
genomic: TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAGgtaatattac ... tattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
EST: gi|163928877|gb|EG711939.1|EG711939
EST:     TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAG                         ATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
genomic: TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAGgtaatattac ... tattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
EST: gi|86479189|gb|CI121822.1|CI121822
EST:     TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAG                         ATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
genomic: TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAGgtaatattac ... tattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
EST: gi|86482468|gb|CI125101.1|CI125101
EST:     TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAG                         ATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
genomic: TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAGgtaatattac ... tattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
EST: gi|87007317|gb|CI278988.1|CI278988
EST:     TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAG                         ATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
genomic: TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAGgtaatattac ... tattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
EST: gi|66913463|gb|CX100311.1|CX100311
EST:     TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAG                         ATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
genomic: TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAGgtaatattac ... tattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
EST: gi|163929507|gb|EG713462.1|EG713462
EST:     TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAG                         ATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
genomic: TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAGgtaatattac ... tattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
EST: gi|29661740|gb|CB658015.1|CB658015
EST:     TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAG                         ATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
genomic: TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAGgtaatattac ... tattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
EST: gi|58688079|gb|CK076766.1|CK076766
EST:     TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAG                         ATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
genomic: TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAGgtaatattac ... tattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
EST: gi|38468259|gb|CF952390.1|CF952390
EST:     TGCTAGGTTACCTGAAGCGGTTAGTCAGTTAAATTATGTTGTTTTACCAG                         ATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
genomic: TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAGgtaatattac ... tattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
EST: gi|86908094|gb|CI298829.1|CI298829
EST:     TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAG                         ATTCCCAGACCAAGAGTAGTCTGATCGGGAAG
genomic: TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAGgtaatattac ... tattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAG
EST: gi|29638321|gb|CB643330.1|CB643330
EST:     TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAG                         ATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG
genomic: TGCTAGGTTACCTGAAGCGGGTAGTCAGTTAAATTATGTTGTTTTACCAGgtaatattac ... tattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacttgtacctgtaattgaacattattgacaagtgtttgtactatattccacagATTCCCAGACCAAGAGTAGTCTGATCGGGAAGCGTTTTGTAAAGATACTGGATTCAATCTCTGCTCCCCCTGCTTTTGCAGCAGCAGAGTTCCCAGCTAG
                        tattgac  putative branch site (score: 2)
             taattgaacattatt  TA-rich tract