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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTTGGAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatctcgaagaatattctaattataagaaaatgtcactgcccatataatatacatacatatgaaagcgatatgtgtttctatatacatattgta...

Basic information

species Oryza sativa
transcript LOC_Os01g55360.3
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55360.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM5G825110_T02 (Zea mays), 5'ss of exon 10
GATTTTGGAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatctcgaagaatattctaattataagaaaatgtcactgcccatataatatacatacatatgaaagcgatatgtgtttctatatacatattgta------
|||||||| ||||||||||||||||||||||| ||||||||  |||||||||| || ||||||| |||| | |||  || ||  |||| | ||||||||||| |       ||| || || | | | |      | |  ||||||  | ||| | ||      
GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGATAGAATGGATTGCCAAgtaagta-tctcaaggaacgttttagctatagggaaatgtcactgacttatggttatccaaacttttaacat-----tctcattctattgaaataatataaaagga

upper sequence: LOC_Os01g55360.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G452529_T03 (Zea mays), 5'ss of exon 2
GATTTTGGAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatctcgaagaatattctaattataagaaaatgtcactgcccatataatatacatacatatgaaagcgatatgtgtttctatatacatattgta----------
|||||||| ||||||||||||||||||||||| ||||||||| ||||||||||||| ||||||| |||| |  ||  ||      ||| | |||||| | || |       ||| ||   |  ||||      | |  |||  | || |  ||| |           
GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAAgtaagta-tctcaagaaacgtt------atagggaaatgttagtgacttatgggtatgca---acttgaataatgcaagctttttaacattctcattctgttgaaataat

upper sequence: LOC_Os01g55360.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT4G26770.1 (Arabidopsis thaliana), 5'ss of exon 9
GATTTTGGAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatctcgaagaatattctaattataagaaaatgtcactgcccatataatatacatacatatgaaagcgatatgtgtt-tctatatacatattgta
||||| |||||||||||||| || ||||| ||  |||||||| |||||||||| || ||||| | || | ||              |   ||| ||       | |||| || |    |    |  || |||    ||||  ||| || ||       
GATTTCGGAGACAGCATACCAGGACATGGAGGATTTACTGACAGAATGGATTGCCAAgtaag-agtcactaa------------cgtcgaaaagtg-------caatatgatctttgcatcgttttaaacgaatcttgttgcctaaatgcag------

upper sequence: LOC_Os01g55360.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv19s0090g01220.t01 (Vitis vinifera), 5'ss of exon 9
GATTTTGGAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatctcgaagaatattctaattataagaaaatgtcactgcccatataatatacatacatatgaaagcgatatgtgtttctatatacatattgta---
||||||||||| || || ||||| |||||||| ||||| ||| |||||||||||||||||||  ||    ||   ||| || |||     | | |     ||    | ||  ||   |   ||         |     || | | | | | |        
GATTTTGGAGATAGTATTCCTGGACATGGTGGAATTACAGACAGAATGGATTGTCAGgtaag--atagaaaattttatactgatttattcatagtaatcatgtttttttatcatcattgtttaatgttattcttgacattcccaca-aaaaaccacgtca

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|29671303|gb|CB667578.1|CB667578
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|88828918|gb|CI073788.1|CI073788
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|86437554|gb|CI119276.1|CI119276
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|89198721|gb|CI003458.1|CI003458
EST:     CTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: CTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|88844663|gb|CI021238.1|CI021238
EST:     CTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: CTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|29679198|gb|CB675473.1|CB675473
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|86504386|gb|CI147019.1|CI147019
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|29681975|gb|CB678250.1|CB678250
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|29671304|gb|CB667579.1|CB667579
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|313081133|gb|HO213719.1|HO213719
EST:     GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: GAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
EST: gi|86433541|gb|CI093884.1|CI093884
EST:     TACTGACCGAATGGATTGTCAG                         ATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC
genomic: TACTGACCGAATGGATTGTCAGgtaagtaatc ... ttttccccagATGGTTATGGCAGTTTTTGCATACATATATCACCAATCATTCATATCGCCC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTTGGAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAGgtaagtaatctcgaagaatattctaattataagaaaatgtcactgcccatataatatacatacatatgaaagcgatatgtgtttctatatacatattgta

- - - - - - - - - - - - - TGGTGG