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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAGTTGTTCTCTATCTGGCTGAGGCTTTAGAATATTGCACCAGCAAGGGGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGATgtgagtatcatatagattgtttttgtaacgtgatcatctgtgtgttttgtaacatttctatgttgtttacatggcacag

Basic information

species Oryza sativa
transcript LOC_Os04g58750.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G382104_T02 (Zea mays), 5'ss of exon 5
AAGAGTTGTTCTCTATCTGGCTGAGGCTTTAGAATATTGCACCAGCAAGGGGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGATgtgagtatcatatagattgtttttgtaacgtgatcatctgtgtgttttgtaacatttctatgttgtttacatggcacag
||| |||||||||| ||| ||||||||||||||||||||||| | || ||| |||||||| ||||||||||| |||||||| |||| ||| |||||||||||||||||| | |   ||||||||  ||| |||||| | ||| ||| |||||||    |||| ||| || ||   ||||
AAGGGTTGTTCTCTGTCTCGCTGAGGCTTTAGAATATTGCACTAACAGGGGCCGTGCTCTCTACCATGATCTCAATGCCTATAGAGCTCTGTTTGATGATgtgagtatcgtgtgatttgttttttcaacatgatcagcagtgggttctgtaacacagttatgctgtctatatactacag

upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA05G37870.1 (Glycine max), 5'ss of exon 6
AAGAGTTGTTCTCTATCTGGCTGAGGCTTTAGAATATTGCACCAGCAAGGGGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGATgtgagtatcatatagattgtttttgtaacgtgatcatctgtgt-----gttttgtaacatttctatgttgtttacatggcacag-------------------
 || |||| ||| |  || ||  | ||| |||| || || |||||||| || ||||| || || |||||||| ||||||||||||||||| | ||||||||| ||| |   ||    |   | ||| || ||| | |   |       |||  |  |   ||  ||| || | | |     |||                   
GAGGGTTGCTCTGTGCCTTGCCCAAGCTCTAGAGTACTGTACCAGCAAAGGACGTGCACTATATCATGATCTGAATGCCTACAGAGTTCTTTATGATGATgtaagttt---attttcttcatctgtgacatgacctttattactcaaggttaaggtattgttggatggtgctcagaacatgcagatatgttaattgtctttta

upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA07G07850.2 (Glycine max), 5'ss of exon 5
AAGAGTTGTTCTCTATCTGGCTGAGGCTTTAGAATATTGCACCAGCAAGGGGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGATgtgagtatc-atatagattgtttttgtaacgtgatcatctgtgtgttttgtaacatttctatgttgtttacatggcacag
||||||||||||  |||| ||  | ||| ||||||| ||||| ||||| ||||||||||| || ||||| || ||||| || |||||||| |||||||| || ||| |   | ||     ||||| ||       ||    |  | ||  ||| |  | | |     ||     |     
AAGAGTTGTTCTACATCTTGCACAAGCTCTAGAATACTGCACAAGCAAAGGGCGTGCTCTCTATCATGACCTCAATGCATATAGAGTTCTTTTTGATGAGgtaagtttttgtgtatcccctttttatacatgtcccaataattagattaataaaaaatgtgttagaattttgcag-----

upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA03G01300.2 (Glycine max), 5'ss of exon 5
AAGAGTTGTTCTCTATCTGGCTGAGGCTTTAGAATATTGCACCAGCAAGGGGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGATgtgagtatcatatagattgtttttgta-acgtgatcatctgtgtgttttgtaacatttctatgttgtttacatggcacag
||||||||||||  |||| ||  | ||| |||| || ||||| ||||| ||||||||||| || ||||| |||||||| || |||||||| |||||||| || ||| |  | |  ||    ||| || || ||  |  || |   |    ||| |     |||| |||   ||    |||
AAGAGTTGTTCTACATCTTGCACAAGCTCTAGAGTACTGCACAAGCAAAGGGCGTGCTCTCTATCATGACCTTAATGCATATAGAGTTCTTTTTGATGAGgtaagt-ttttgtgtatcccctttttatacatgtcc--ctataattagattaataaaaaaatgt-gttagaattttgcag

upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA08G01730.2 (Glycine max), 5'ss of exon 5
AAGAGTTGTTCTCTATCTGGCTGAGGCTTTAGAATATTGCACCAGCAAGGGGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGATgtgagt--atcatatagattgtttttgtaacgtgatcatctgtgtgttttgtaacatttctatgttgtttacatggcacag---------------------
 ||||||| ||| |  || ||  | ||| |||| || || |||||||| || |||||||| || |||||||| ||||| ||||||||||| | ||||||||| |||  ||  | |  ||   |    | || | || ||    | |||  | ||   ||  ||| || | |  || ||                        
GAGAGTTGCTCTGTGCCTTGCCCAAGCTCTAGAGTACTGTACCAGCAAAGGACGTGCTCTATATCATGATCTGAATGCTTACAGAGTTCTTTATGATGATgtaagtttattttcttcatctgtgacatgaccttattattcaag-gttaaggaattgttggatgatgctcatctg-catgttaattgtcttttattcttatg

upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G63500.1 (Arabidopsis thaliana), 5'ss of exon 4
AAGAGTTGTTCTCTATCTGGCTGAGGCTTTAGAATATTGCACCAGCAAGGGGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGATgtgagta----tcatatagattgtttttgtaacgtgatcatctg----tgtgttttgtaacatttctatgttgtttacatggcacag----------------------------------------
|||||| | | |  || | ||| | |||||||||||||| ||  |||| || ||||| || ||||||||  | ||||| || |||||||||||||||||||| |||     | || |  ||| | |||    |  ||| |  |     | | | ||  |  |||| ||   | | |  |||  |  |                                        
AAGAGTAGCTTTACATATTGCTCAAGCTTTAGAATATTGTACTGGCAAAGGACGTGCACTCTACCATGACTTAAATGCTTATAGAGTTCTCTTTGATGATgtaagttaagcttatttttattttattttgggcaagataagttaagcttatatgtttgattatttttaacgtttgtcaatgttaatgtgtgaatatagaaacatcatcatatgttttgtgtttttag

upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G41260.1 (Arabidopsis thaliana), 5'ss of exon 4
AAGAGTTGTTCTCTATCTGGCTGAGGCTTTAGAATATTGCACCAGCAAGGGGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGATgtgagtatcatatagattgtttt-tgtaacgtgatcatct-gtgtgttttgtaacatttctatgttgtttacatggcacag
 ||||| | | |  || | ||| ||||  |||| ||||| |||||||| || ||||| || |||||||| || ||||| || |||||||||||||||||||| ||| | ||| ||||| ||||   |   ||     ||  |||| | |   || | || |||||| |||   |   |   
GAGAGTAGCTTTGCATATTGCTCAGGCGCTAGAGTATTGTACCAGCAAAGGACGTGCACTTTACCATGACCTAAATGCTTATAGAGTTCTCTTTGATGATgtaagtttgatacagatttttttacctttggtttctgtcaagtgtatatgagaataattttatgtt-tttgtttcttag--

upper sequence: LOC_Os04g58750.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv02s0025g03550.t01 (Vitis vinifera), 5'ss of exon 6
AAGAGTTGTTCTCTATCTGGCTGAGGCTTTAGAATATTGCACCAGCAAGGGGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGATgtgagtatcatatagattgtttttgtaacgtgatcatctgtgtgttttgtaacatttct---atgttgtttacatggcacag---
||| || | | | ||||| ||  | ||||| |||||||| |||||||| || ||||| || || |||||||||||||| || ||| || | ||||||||||| |||||  |     || |   | | | |  ||  | | | | | || ||  || | |   |  ||| |   ||   |      
AAGGGTGGCTTTATATCTTGCACAAGCTTTGGAATATTGTACCAGCAAAGGACGTGCACTTTATCATGATCTTAATGCTTATAGAATTGTTTTTGATGATgtaagtatgttgctttttttcaattttatggtattttttttttctcttttagaatctttgatacattgctcttattaaatctcag

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|33794016|gb|CF322898.1|CF322898
EST:     GGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGAT                         GACTGTAACCCTAGGCTTTCATGTTTTGGCCTCATGAAGAACAGTCGAGAT
genomic: GGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGATgtgagtatca ... catggcacagGACTGTAACCCTAGGCTTTCATGTTTTGGCCTCATGAAGAACAGTCGAGAT
EST: gi|33675914|gb|CF304153.1|CF304153
EST:     GGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGAT                         GACTGTAACCCTAGGCTTTCATGTTTTGGCCTCATGAAGAACAGTCGAGAT
genomic: GGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGATgtgagtatca ... catggcacagGACTGTAACCCTAGGCTTTCATGTTTTGGCCTCATGAAGAACAGTCGAGAT
EST: gi|29624788|gb|CB629799.1|CB629799
EST:     GGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGAT                         GACTGTAACCCTAGGCTTTCATGTTTTGGCCTCATGAAGAACAGTCGAGAT
genomic: GGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGATgtgagtatca ... catggcacagGACTGTAACCCTAGGCTTTCATGTTTTGGCCTCATGAAGAACAGTCGAGAT
EST: gi|58669011|gb|CK057697.1|CK057697
EST:     GGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGAT                         GACTGTAACCCTAGGGCTTT
genomic: GGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGATgtgagtatca ... catggcacagGACTGTAACCCTAGG-CTTT
EST: gi|58656214|gb|CK044894.1|CK044894
EST:     GGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGAT                         GACTGTAACCCTAGGCTTTCATGTTTTGGCCTCATGAAGAACAGTCGAGAT
genomic: GGCGTGCTCTGTACCATGATCTTAATGCCTACAGAGTTCTCTTTGATGATgtgagtatca ... catggcacagGACTGTAACCCTAGGCTTTCATGTTTTGGCCTCATGAAGAACAGTCGAGAT