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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacatgtgcatcaagaaggcttcctttcatgttttggatggtcagaatttaatattgaattactaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT

Basic information

species Oryza sativa
transcript LOC_Os01g62080.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 5
gtaagtacatgtgcatcaagaaggcttcctttca--tgttttggatggtcagaatttaatattgaattactaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
||||||  || ||| |||||||||||    || |  |||||| |||| ||||  | | ||||||||||  | |  |  |||||||||||||| ||| || |||||| |||||||||| || ||||||||||| || ||| ||||||| || |||||||| || |||||||||||||||||||
gtaagtgaatatgcgtcaagaaggctatactttacttgtttttgatgatcaggttatgatattgaattgatgatctcttcagGTATTTGAGAAGCTTGGGCCAAGCCTATATGACTTTCTGCGAAAGAATAGCTACCGTTCATTTCCTATTGACCTTGTCCGAGAATTTGCCAGACAAATAT

upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G35800.1 (Glycine max), 3'ss of exon 3
--------------gtaagtacatgtgcatcaag---aaggcttcctttcatgttttggatggtcagaatttaatattgaattac-taactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
               ||  |  |  |  || ||    | |  |     | ||  |  |  | |  | | ||    || || |||  |   ||   ||||||||||||| ||| |||||||||||||| || || ||||| || || | ||||||| | ||  | || || ||||||||||| |||| ||||||| | |
gtaagtatttattgatatttgtaatttgattaaatgaaggaatgtgcattatcatgcgagttgaaaaacttgtggatggatttaaatggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATACGATTTTCTCCGCAAAAACAATTATCGTTCTTTATCAATTGATCTTGTTCGGGAGTTTGGCAGACAACTTT

upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G33100.1 (Glycine max), 3'ss of exon 5
-----------------------------gtaagt-acatgtgcatcaaga-aggcttcctttcatgttttggatggtcagaa-tttaatattgaatt--actaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
                              ||| | ||| |    || |   |  | | |||  || || ||   | | | ||  ||     || |||  | |   ||   ||||||||||||| ||| ||||||||||||||||| || ||||| || || || |||||| | ||||| || || ||||||||||| |||| ||||||| | |
gtaagtatttattgatatttgtaatttaattaaatgacaggaatgtctattcaatcatgcttaaatattctgtgagttaaaaaacttgcggatggatttaaatggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATATGATTTTCTCCGCAAAAACAGCTATCGTTCTTTTCCTATTGATCTTGTTCGGGAGTTTGGCAGACAACTTT

upper sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G53570.4 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------gtaagtacatgtgcatcaagaaggcttcct---ttcatgttttggatggtc----agaatttaatattgaatt--actaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
                         ||||    | | |  | | |   |         ||  | ||   ||       |||| ||     ||  ||  | |   ||   ||||||||||||| ||| ||||||||||||||||| || ||||| || || || || ||| ||||||| || || |||||||||||  ||| ||||||| | |
gtaagtgctgttacctttatttgacaagtttgaggggaaaatgcaatttcttcacgcccaaatgttatgtgagttaaaagaacttgcgcatgggtttaaatggtttcaacagGTATTTGAGAAGCTTGGACCAAGCTTATATGATTTTCTCCGCAAAAACAGCTACCGTTCATTTCCCATTGATCTTGTTCGGGAGCTTGGCAGACAACTTT

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|117243444|gb|CT848361.1|CT848361
EST:     CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA                         GTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
genomic: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAgtaagtacat ... actttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
EST: gi|58654607|gb|CK043287.1|CK043287
EST:     CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA                         GTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
genomic: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAgtaagtacat ... actttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
EST: gi|29665089|gb|CB661364.1|CB661364
EST:     CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA                         GTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
genomic: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAgtaagtacat ... actttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
EST: gi|29679261|gb|CB675536.1|CB675536
EST:     CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATA                         GTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT
genomic: CTGTGTGCAAATACGGAATTGGTTTGACTATCGTAATCATATATGTATAgtaagtacat ... actttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctttcatgttttggatggtcagaatttaatattgaattactaactttgtcagGTATTTGAGAGGCTCGGACCAAGCTTATATGACTTCCTCCGAAAGAATAGTTATCGTGCATTTCCGATCGACCTTGTTCGGGAATTTGCCAGACAAATAT
                                        tactaac  putative branch site (score: 0)
                                              ctttgtc  CT-rich tract
                       agaatttaatattgaa  TA-rich tract