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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCTGCATTTAATAGAAACAGGCAAAACAACAGGGTGGCGATATTTCGAGACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAGgtccgtttaacgtaataaactttatttttgtaactctttagctatagaatgttttgccattccaccgtacagttcctatttattattggtgaaccattta...

Basic information

species Oryza sativa
transcript LOC_Os09g39462.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g39462.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G103345_T01 (Zea mays), 5'ss of exon 2
ATCCTGCATTTAATAGAAACAGGCAAAACAACAGGGTGGCGATATTTCGAGACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAGgtccgtttaacgtaataaactttatttttgtaactctttagctatagaatgtttt-gccattccaccgtacagttcctatttattattggtgaaccattta-
| |||||| | |||||||||| ||| ||||| ||||| || || ||  |||| ||||||||||| |||||||||||||||||||||||||||||||||||||| ||||    |     |    || | | | |  ||  |    ||| |     | | ||    | | |  | |  |||||| |||        |   |   
AGCCTGCAGTCAATAGAAACAAGCAGAACAATAGGGTTGCAATTTTCAGAGATCGTGAGTCAGAGCGCAAGGATCCTGATTATGACAGAAGCTATGACAGgtcagtttcttttgtcgtaacacatctctttgatgctaaactcttagcacaccgtagacaggaaatctttta-tggctattt-ttaccatgcttctgctccg

upper sequence: LOC_Os09g39462.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G009575_T01 (Zea mays), 5'ss of exon 3
ATCCTGCATTTAATAGAAACAGGCAAAACAACAGGGTGGCGATATTTCGAGACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAGgtccgtttaacgtaataaactttatttttgtaactctttagctatagaatgttttgc-cattccaccgtacagttcctatttattattggtgaaccattta
| |||||| | ||||||||||| || ||||| ||||| || || ||  |||||||||||||||| |||| ||||||||||||||||||||||||||||||||  ||||    |  |  |    || | | |    || ||    |||       ||  ||    | | |  | |  |||||| |||        |   | |
AGCCTGCAGTCAATAGAAACAGACAGAACAATAGGGTTGCAATTTTCAGAGACCGTGAGTCAGAGCGCAGGGATCCTGATTATGACAGAAGCTATGACAGgttagttttttttcttgtaacacatctctttgctgctatactcctagcgcaccatgaacaagaaaacttttattggctattt-ttaccatgcttctgctca

upper sequence: LOC_Os09g39462.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA20G32800.2 (Glycine max), 5'ss of exon 2
ATCCTGCATTTAATAGAAACAGGCAAAACAACAGGGTGGCGATATTTCGAGACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAGgtccgtttaacgtaataaactttatttttgtaactctttagctatagaatgttttgccattccaccgtacagttcctatttattattggtgaaccattta-------
|     || ||  |||  ||||||||||||| |||||||| |||||||| |||||||||   || ||||| ||||||||||||||||| | |||||| ||||  || |  | |        ||| |  || |    |||  || |  |  ||||||  |       ||   |||||| ||| | |    | ||   |||        
AGGAGCCAGTTGGTAGGTACAGGCAAAACAATAGGGTGGCTATATTTCGGGACCGTGAGGTTGACCGCAAAGATCCTGATTATGACAGGAACTATGATAGgtatgtgtgccttttacctagttagtcatgca----tttgtctgttaa--gttttgtgaccttgttgtcttgttcctctttgtcaa-aataaatggttttagtttgc

upper sequence: LOC_Os09g39462.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA10G34810.3 (Glycine max), 5'ss of exon 2
ATCCTGCATTTAATAGAAACAGGCAAAACAACAGGGTGGCGATATTTCGAGACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAGgtccgtttaacgtaataaactttatttttgtaactctttagctatagaatgttttgccattccaccgtacagttcctatttattattggtgaaccattta-------
|     || ||  |||  |||||||||| || |||||||| |||||||| ||||| |||   || ||||| ||||||||||||||||| | |||||| ||||  ||  | | |     |  ||| |  ||     ||||  || |  |  ||||||  |       ||   |||||| ||| | |   || ||   ||||       
AGGAGCCAGTTGGTAGGTACAGGCAAAATAATAGGGTGGCTATATTTCGGGACCGAGAGGTTGACCGCAAAGATCCTGATTATGACAGGAACTATGATAGgtatgtgcaccttttaccatgttagtcatga----ctttgtctgttaa--gttttgtgacctttttgtcttgttcctctttgtcaa-agtaaatggtttaagtttgc

upper sequence: LOC_Os09g39462.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv13s0106g00640.t01 (Vitis vinifera), 5'ss of exon 2
ATCCTGCATTTAATAGAAACAGGCAAAACAACAGGGTGGCGATATTTCGAGACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAGgt---ccgtttaacgtaataaactttatttttgtaactctttagctatagaatg-ttttgccattccaccgtacagttcctatttattattggtgaaccattta
|     || ||  |||  |||  | ||| || |||||||| || ||||| |||||||||   || || |||||||||||||||||||| |||||||| ||||   | ||| |   | ||        || || |   | ||||  |||    ||  |||    || ||    | |      ||||  ||||  ||||  ||   
AGGAGCCAATTGGTAGGTACAAACCAAATAATAGGGTGGCTATCTTTCGGGACCGTGAGATTGACCGTAAGGATCCTGATTATGACAGGAGCTATGATAGgtatgctgttaactcttatttgtccatttcttatctttatttaattattttttggcttttttttttcaaaaaaaaaaaaaaattttgtattattgaat-at---

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|58654486|gb|CK043166.1|CK043166
EST:     GACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAG                         GTACATGCAAAGATTTGATCCTGGATTTGGATTTAATGGAGGTTCATACAC
genomic: GACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAGgtccgtttaa ... ggctttacagGTACATGCAAAGATTTGATCCTGGATTTGGATTTAATGGAGGTTCATACAC
EST: gi|58653672|gb|CK042352.1|CK042352
EST:     GACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAG                         GTACATGCAAAGATTTGATCCTGGATTTGGATTTAATGGAGGTTCATACAC
genomic: GACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAGgtccgtttaa ... ggctttacagGTACATGCAAAGATTTGATCCTGGATTTGGATTTAATGGAGGTTCATACAC
EST: gi|29682111|gb|CB678386.1|CB678386
EST:     GACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAG                         GTACATGCAAAGATTTGATCCTGGATTTGGATTTAATGGAGGTTCATACAC
genomic: GACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAGgtccgtttaa ... ggctttacagGTACATGCAAAGATTTGATCCTGGATTTGGATTTAATGGAGGTTCATACAC
EST: gi|58660413|gb|CK049093.1|CK049093
EST:     CGCAAGGATCCTGATTATGACAGAAGCTATGACAG                         GTACATGCAAAGATTTGATCCTGGATTTGGATTTAATGGAGGTTCATACAC
genomic: CGCAAGGATCCTGATTATGACAGAAGCTATGACAGgtccgtttaa ... ggctttacagGTACATGCAAAGATTTGATCCTGGATTTGGATTTAATGGAGGTTCATACAC
EST: gi|58606100|gb|CK034133.1|CK034133
EST:     GACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAG                         GTACATGCAAAGATTTGATCCTGGATTTGGATTTAATGGAGGTTCATACAC
genomic: GACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAGgtccgtttaa ... ggctttacagGTACATGCAAAGATTTGATCCTGGATTTGGATTTAATGGAGGTTCATACAC
EST: gi|58659833|gb|CK048513.1|CK048513
EST:     GACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAG                         GTACATGCAAAGATTTGATCCTGGATTTGGATTTAATGGAGGTTCATACAC
genomic: GACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAGgtccgtttaa ... ggctttacagGTACATGCAAAGATTTGATCCTGGATTTGGATTTAATGGAGGTTCATACAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCTGCATTTAATAGAAACAGGCAAAACAACAGGGTGGCGATATTTCGAGACCGTGAGTCAGATCGCAAGGATCCTGATTATGACAGAAGCTATGACAGgtccgtttaacgtaataaactttatttttgtaactctttagctatagaatgttttgccattccaccgtacagttcctatttattattggtgaaccattta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC