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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgtatgttgcctacaatctccttatttggatctagtgatgtgctgtccaacctccattccgtcttttttttaagcatgtttgccaaatttattctttgtgt...

Basic information

species Oryza sativa
transcript LOC_Os03g15780.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g15780.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G161337_T03 (Zea mays), 5'ss of exon 2
GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgt-atgttgcctacaatctccttatttggatctagtgatgtgctgtccaacctccattccgtcttttttttaagcatgtttgccaaatttatt-ctttgtgt----
|| |||||| ||||||||||||||||||| |||||||||||| || |||| || ||||| ||||||||||| ||||| ||||||||||| | |||| | |||| | ||||||||||||| || | || | | | | | |||| | | | |||||||||||||||| | | | ||
GTTAGTGGACAGTTGGATGATCATCTCCAGAGTTGGGATGCCTTGAGAGCTGCCTTGCCCGTTGGAACAGTCAGTGGTGCACCAAAGgtgaagttgtttccaatattcttatttggatct-----tgaaccttcactcatgtaatatattttttgtgtga-catgtttgccaaattttctgcctcttgatata

upper sequence: LOC_Os03g15780.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA18G03260.1 (Glycine max), 5'ss of exon 10
GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgtatgttgcctaca-atctcctt--------atttggatctagtgatgtgctgtccaacctccattc----------cgtcttttttttaagcatgtttgccaaatttattctttgtgt--------------------------------------------------------------
|| | |||||||||| | |||||| | || ||||||||||||||||| || |||||||||||||| || |||||||| |||||||| ||| | | |||||| | || || | | | | | | | | || ||| |||| || | || | || ||| |
GTTACTGGAGAGTTGCAAGATCATTTGACTAGCTGGGATGCCCTGCGAGCTGCATTGCCTGTTGGAACTGTCAGTGGAGCGCCAAAGgtttgtaattttcttgactcctttttagtcaacttagacaaaacattttatgttttcgcttttaattacaaaattgtcgccttgttttcaaataggtaaacgaacttttaattacagaaagcagtgaaaataacttttcaaaacttgccaccttgattcgttcttttatgtggatatgcag

upper sequence: LOC_Os03g15780.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA18G03270.1 (Glycine max), 5'ss of exon 9
GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgtatgttgcctac--aatctccttatttggatctagtgatgtg----ctgtccaacctccattccgtcttttttttaagcatgtttgccaaatttattctttgtgt----------------------------------------------------------------------
|| | |||||||||| | || ||| | || ||||||||||||||||| || ||||| |||||||| || ||||||||||||||||| ||| | | | || || | | ||| ||| | | | | |||| ||| ||||||| | || | ||| | ||| || |
GTTACTGGAGAGTTGCAAGAGCATTTGACTAGCTGGGATGCCCTGCGAGCTGCATTGCCCGTTGGAACTGTCAGTGGAGCACCAAAGgtttgtaattttctcgacttctttttagtcaactacgaatgagaaaacgtttttgttttcattt--tctgttttttacttttaattacaaaactgtttccttacttccaatctatttcctgttttgaaatatgtgttcaaaactttccaccttgattcattcttatgtggatgcag

upper sequence: LOC_Os03g15780.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv06s0004g06320.t01 (Vitis vinifera), 5'ss of exon 10
GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgtatgttgcctacaatc----tccttatttggatctagtgatgtgctgtccaacctccattccgtcttttttttaagcatgt---ttgccaaatttattctttgtgt----------------------------------------------------------------------------------------
|| | |||||| || ||||||| | || |||||||| || || || || ||||||||||||||||||||||| |||||||||||||| | ||| | ||||| | | | | |||| |||| | || || | || | | ||| ||| | || | | |
GTTACTGGAGAATTACTTGATCATTTAACCAGCTGGGATGCTCTACGTGCTGCATTGCCTGTTGGAACAGTTAGTGGGGCACCAAAGgtatgcacgcaccaaccgccttccttctctaattacacatttgtggtgtctggttgtttgtggtcctgagttgtgaggaaataaattgtcaagtccatccaggctttcacgagtacgctaatgcatgatctatgtacctgttttcatgagggtccattttatgtcgatgacattgtcagctctgctacaatacag

upper sequence: LOC_Os03g15780.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv13s0067g00400.t01 (Vitis vinifera), 5'ss of exon 10
GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgtatgttgcctacaatctccttatttggatctagtgatgtgctgtccaacctccattccgtcttttttttaagcatgtt-tgccaaatttattctttgtgt-----
|| | || |||||| | ||||||||| || ||| |||||||||| ||| ||||||| |||||||||||||||||||||| || | || | | | || | | || | |||| | | || ||| |||| || | | || || || | | || | ||
GTTACAGGGGAGTTGCAAGATCATCTCACTAGCTGGAATGCCCTGCGCAGTATACTGCATGTTGGAGCAGTTAGTGGAGCACCAAAGgttacttattttgcatattc--actttgct---atggtttgctttttattctgcatgtt-tcttgttctagaccaggtgatgaaatacttgtggattaaaaacttg

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|29624822|gb|CB629833.1|CB629833
EST:     ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCCCCAAAG                         GTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
genomic: ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgtatgttgcc ... acataaccagGTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
EST: gi|29616792|gb|CB621804.1|CB621804
EST:     ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG                         GTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
genomic: ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgtatgttgcc ... acataaccagGTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
EST: gi|86485602|gb|CI128235.1|CI128235
EST:     GTTAGTGGAGCACCAAAG                         GTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
genomic: GTTAGTGGAGCACCAAAGgtatgttgcc ... acataaccagGTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
EST: gi|29616044|gb|CB621056.1|CB621056
EST:     ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG                         GTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
genomic: ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgtatgttgcc ... acataaccagGTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
EST: gi|29662736|gb|CB659011.1|CB659011
EST:     ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG                         GTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
genomic: ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgtatgttgcc ... acataaccagGTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
EST: gi|29646546|gb|CB651553.1|CB651553
EST:     ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG                         GTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
genomic: ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgtatgttgcc ... acataaccagGTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
EST: gi|29662735|gb|CB659010.1|CB659010
EST:     ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG                         GTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
genomic: ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgtatgttgcc ... acataaccagGTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
EST: gi|25803679|gb|CA759640.1|CA759640
EST:     ATGCCCTGCGANCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG                         GTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
genomic: ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgtatgttgcc ... acataaccagGTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
EST: gi|29628879|gb|CB633890.1|CB633890
EST:     ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG                         GTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
genomic: ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgtatgttgcc ... acataaccagGTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
EST: gi|29614551|gb|CB619564.1|CB619564
EST:     ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAG                         GTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA
genomic: ATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgtatgttgcc ... acataaccagGTGAAAGCCATGGAGCTGATAGACGAGCTAGAGGTCACAAGACGAGGACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAGTGGAGAGTTGGATGATCATCTCCAAAGTTGGGATGCCCTGCGAGCCGCGTTGCCTGTTGGAACAGTTAGTGGAGCACCAAAGgtatgttgcctacaatctccttatttggatctagtgatgtgctgtccaacctccattccgtcttttttttaagcatgtttgccaaatttattctttgtgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA