Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccagaggcatttttctcgctttgctaaaatttattgtctgagaaaggttatttgaacattataattattaattctcttcatttctaatacttttgtagCCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACGAAGGCCAAATATGCAACCTGGTCCTGTAAATTCTGTACTCTAGAAAACA

Basic information

species Oryza sativa
transcript LOC_Os06g09170.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g09170.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G061472_T01 (Zea mays), 3'ss of exon 2
taccagaggcatttttc-tcgctttgctaaaatt-tattgtctgagaaaggttatttgaacattataattattaattctcttcatttctaatacttttgtagCCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACGAAGGCCAAATATGCAACCTGGTCCTGTAAATTCTGTACTCTAGAAAACA
||     | | | || | | | |||  |   | |  |   | |    |||||||||  | |||  |  |   |||  | || |     |   || | || ||||||||||||||||||||||||||||| |  || | ||||||||||   | ||||| || ||  |||| ||||| |||||||| ||||||||||| ||||
tagtcttgacttcttccatagtttttttcctactacacattttacttaaggttatt--atcatgcttttctctaacacactgcgaaatttgaacctatgcagCCTCTGGCACCAATCTGTGAAGTTTGTGGTACAACAAAACCTAAAATTGCAAAGGCGAAGTACACAACTTGGTCTTGTAAATTTTGTACTCTAGAGAACA
















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|88529068|gb|CI456395.1|CI456395
EST:     GTGTGTTGCTTGCACACTTTTAAATCAG                         CCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACG
genomic: GTGTGTTGCTTGCACACTTCTAAATCAGgtatgttttc ... acttttgtagCCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACG
EST: gi|88528435|gb|CI456671.1|CI456671
EST:     CAGGAGATAGTTCTCTATGGGAGTGTGTTGCTTGCACACTTCTAAATCAG                         CCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACG
genomic: CAGGAGATAGTTCTCTATGGGAGTGTGTTGCTTGCACACTTCTAAATCAGgtatgttttc ... acttttgtagCCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACG
EST: gi|88542322|gb|CI471644.1|CI471644
EST:     GGGAGTGTGTTGCTTGCACACTTCTAAATCAG                         CCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACG
genomic: GGGAGTGTGTTGCTTGCACACTTCTAAATCAGgtatgttttc ... acttttgtagCCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACG
EST: gi|86858727|gb|CI275009.1|CI275009
EST:     CAGGAGATAGTTCTCTATGGGAGTGTGTTGCTTGCACACTTCTAAATCAG                         CCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACG
genomic: CAGGAGATAGTTCTCTATGGGAGTGTGTTGCTTGCACACTTCTAAATCAGgtatgttttc ... acttttgtagCCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACG
EST: gi|86415305|gb|CI069708.1|CI069708
EST:     CAGGAGATAGTTCTCTATGGGAGTGTGTTGCTTGCACACTTCTAAATCAG                         CCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACG
genomic: CAGGAGATAGTTCTCTATGGGAGTGTGTTGCTTGCACACTTCTAAATCAGgtatgttttc ... acttttgtagCCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACG
EST: gi|88529597|gb|CI457931.1|CI457931
EST:     GCTTGCACACTTCTAAATCAG                         CCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACG
genomic: GCTTGCACACTTCTAAATCAGgtatgttttc ... acttttgtagCCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACG
EST: gi|88907996|gb|CI090592.1|CI090592
EST:     TGCACACTTCTAAATCAG                         CCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACG
genomic: TGCACACTTCTAAATCAGgtatgttttc ... acttttgtagCCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggttatttgaacattataattattaattctcttcatttctaatacttttgtagCCTCTGGCACCAATCTGTGAAGTTTGTAGCGCAGCTAAACCTAAAACCACGAAGGCCAAATATGCAACCTGGTCCTGTAAATTCTGTACTCTAGAAAACA
                                      ttctaat  putative branch site (score: 2)
                                            tactttt  CT-rich tract
              attataattattaatt  TA-rich tract