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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgttcttttatttgctcacctaatatgtccaatacaactaagcctaactatatgattatctgttatttcagAATTGTAGCCTATCTATCTCGTGTTCTCGAGGTTGCATTCAGTGCTCTAGAAGGTCTCAATAAACAGTCCTTTTTGACTGAGCTG

Basic information

species Oryza sativa
transcript LOC_Os12g13590.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM5G823484_T01 (Zea mays), 3'ss of exon 5
gtgttcttttatttgctcacctaatatgtccaatacaactaagcctaactatatgattatctgttatttcagAATTGTAGCCTATCTATCTCGTGTTCTCGAGGTTGCATTCAGTGCTCTAGAAGGTCTCAATAAACAGTCCTTTTTGACTGAGCTG
||  | || | | |        ||| || |   | | | ||   |||||| | || || || ||| || |||||||||||||||||| ||||||||||| ||||||||||||||||| || ||||| ||||| ||||||||||||||||||||||||
gtagttttctttctatctttaaaatttgccatgtcccaatataactaact-tctgtttctcggttgtt-cagAATTGTAGCCTATCTCTCTCGTGTTCTTGAGGTTGCATTCAGTGCCCTTGAAGGCCTCAACAAACAGTCCTTTTTGACTGAGCTG

upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv15s0046g02200.t01 (Vitis vinifera), 3'ss of exon 19
-------------------------gtgttcttttatttgctcacctaatatgtccaatacaactaagcct-aactatatgattatctgttatt--tcagAATTGTAGCCTATCTATCTCGTGTTCTCGAGGTTGCATTCAGTGCTCTAGAAGGTCTCAATAAACAGTCCTTTTTGACTGAGCTG
                         | |     | |||   | |  |||| |      | |  |      | || |   |  || |||    ||    ||| |||| || ||||| |||||||| || |||| |||||||| ||| ||||||||||| ||||| ||  | ||  |||||||  ||
cattttacatgaagaatctgcaatagagagtcataattgttttatttaattttcttgttccttccggatgtcaattgatttcttttcttcccttgactagAGTTGTGGCATATCTTTCTCGTGTGCTTGAGGCTGCATTCACTGCCCTAGAAGGTCTTAATAAGCAAGCTTTCCTGACTGAATTG
















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|33822211|gb|CF336920.1|CF336920
EST:     CCAGATGATGGAGCTGCACCGGATCATCGACCGACCAATGCTTGCATAAG                         AATTGTAGCCTATCTATCTCGTGTTCTCGACGTTGCATTCAGTGC
genomic: CCAGATGATGGAGCTGCACCGGATCATCGACCAACCAATGCTTGCATAAGgtgttctttt ... gttatttcagAATTGTAGCCTATCTATCTCGTGTTCTCGAGGTTGCATTCAGTGC
EST: gi|66920327|gb|CX107175.1|CX107175
EST:     CCAGATGATGGAGCTGCACCGGATCATCGACCAACCAATGCTTGCATAAG                         AATTGTAGCCTATCTATCTCGTGTTCTCGAGGTTGCATTCAGTGCTCTAGA
genomic: CCAGATGATGGAGCTGCACCGGATCATCGACCAACCAATGCTTGCATAAGgtgttctttt ... gttatttcagAATTGTAGCCTATCTATCTCGTGTTCTCGAGGTTGCATTCAGTGCTCTAGA
EST: gi|29669745|gb|CB666020.1|CB666020
EST:     CCAGATGATGGAGCTGCACCGGATCATCGACCAACCAATGCTTGCATAAG                         AATTGTAGCCTATCTATCTCGTGTTCTCGA
genomic: CCAGATGATGGAGCTGCACCGGATCATCGACCAACCAATGCTTGCATAAGgtgttctttt ... gttatttcagAATTGTAGCCTATCTATCTCGTGTTCTCGA
EST: gi|33822202|gb|CF336916.1|CF336916
EST:     CCAGATGATGGAGCTGCACCGGATCATCGACCGACCAATGCTTGCATAAG                         AATTGTAGCCTATCTATCTCGTGTTCTCGACGTTGCATTCA
genomic: CCAGATGATGGAGCTGCACCGGATCATCGACCAACCAATGCTTGCATAAGgtgttctttt ... gttatttcagAATTGTAGCCTATCTATCTCGTGTTCTCGAGGTTGCATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacctaatatgtccaatacaactaagcctaactatatgattatctgttatttcagAATTGTAGCCTATCTATCTCGTGTTCTCGAGGTTGCATTCAGTGCTCTAGAAGGTCTCAATAAACAGTCCTTTTTGACTGAGCTG
                         gcctaac  putative branch site (score: 2)
                                              ttatttc  putative PPT
                            taactatatgattat  TA-rich tract