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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcccctcataactcgtcttcaggagccatttctttgcgtggcagccttgaacttaactcaaagcctgtcttggacagTCCACGGCTTCTTACAAAGCTGCGGCTCGGCTTGCAAGTGCTACTCCACCTCCAGCACATATCCTCAGTAGAGGCATTGGGTGGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g55500.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55500.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G437859_T02 (Zea mays), 3'ss of exon 8
gtaatgcccctcataactcgtcttcaggagccatttctttgcgtggcagccttgaacttaactcaaag--cctgtcttggacagTCCACGGCTTCTTACAAAGCTGCGGCTCGGCTTGCAAGTGCTACTCCACCTCCAGCACATATCCTCAGTAGAGGCATTGGGTGGCAG
|| | |  ||  |||  | || ||      |||||     ||| | |     ||| |||||| ||| |  ||| ||||||||||||||| || || |||||||| || ||||| ||||| ||||| ||||||||||| || || |||||||| ||||||||||||||||||
gtgaggatcc--atattttgttttggaatcccattcgggagcgggaccaaactgaccttaacgcaatgtgcctctcttggacagTCCACAGCCTCCTACAAAGCCGCTGCTCGTCTTGCGAGTGCGACTCCACCTCCGGCTCACATCCTCAGCAGAGGCATTGGGTGGCAG
















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|58669485|gb|CK058171.1|CK058171
EST:     CCGGTCAATCCTTTGGTATGGTATCTGCTGTTCTGGTATCGCTAGTAGAG                         TCCACGGCTTCTTACAAAGCTGCGGCTCGGCTTGCAAGTGCTACTCCACCT
genomic: CCGGTCAATCCTTTGGTATGGTATCTGCTGTTCTGGTATCGCTAGTAGAGgtaatgcccc ... tcttggacagTCCACGGCTTCTTACAAAGCTGCGGCTCGGCTTGCAAGTGCTACTCCACCT
EST: gi|33793472|gb|CF322619.1|CF322619
EST:     CCGGTCAATCCTTTGGTATGGTATCTGCTGTTCTGGTATCGCTAGTAGAG                         TCCACGGCTTCTTACAAAGCTGCGGCTCGGCTTGCAAGTGCTACTCCACCT
genomic: CCGGTCAATCCTTTGGTATGGTATCTGCTGTTCTGGTATCGCTAGTAGAGgtaatgcccc ... tcttggacagTCCACGGCTTCTTACAAAGCTGCGGCTCGGCTTGCAAGTGCTACTCCACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagccatttctttgcgtggcagccttgaacttaactcaaagcctgtcttggacagTCCACGGCTTCTTACAAAGCTGCGGCTCGGCTTGCAAGTGCTACTCCACCTCCAGCACATATCCTCAGTAGAGGCATTGGGTGGCAG
                            acttaac  putative branch site (score: 3)
                                         cctgtctt  putative PPT
     atttcttt  TA-rich tract