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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTATGATCCACGTCCTGTTCAACCTGATTCTCTCTTTCCAGTTTTTTCAGTGACAAAGGGTATCACTGCTGGCATGGTGCATTGGCTTGTTGACAAAGGgtgagtgcttaatcacaatgccaagttttttttttcttaacatgctagtgtaaatatgtttgcaggccgtcgtattacagtacattatactacctcagat...

Basic information

species Oryza sativa
transcript LOC_Os06g48770.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g48770.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G140917_T01 (Zea mays), 5'ss of exon 16
AGTATGATCCACGTCCTGTTCAACCTGATTCTCTCTTTCCAGTTTTTTCAGTGACAAAGGGTATCACTGCTGGCATGGTGCATTGGCTTGTTGACAAAGGgtgagtgcttaatcacaatgccaagttttttttttcttaacatgctagtgtaaatatgtttgcaggccgtcgtattacagtacattatactacctcagat------
|||||||||| || |||||||||||||||||||| ||||| ||||| |||||||| ||||||||||||||||| ||||| ||||||||||| ||||||||||||||  |||||  || |||||||||| ||||  | |    |||  || ||||| | | |||| |   | |   |||| || |||| |  |       |      
AGTATGATCCCCGACCTGTTCAACCTGATTCTCTTTTTCCTGTTTTCTCAGTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGGgtgagta-ttaatt-cagtgccaagtttcttttaacct----tgcctgtttaaatctatctgcatgatattggtgtacactatattacagaattcggtgtgcttat

upper sequence: LOC_Os06g48770.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA14G20110.1 (Glycine max), 5'ss of exon 15
AGTATGATCCACGTCCTGTTCAACCTGATTCTCTCTTTCCAGTTTTTTCAGTGACAAAGGGTATCACTGCTGGCATGGTGCATTGGCTTGTTGACAAAGGgtgagtgcttaatcacaatg-ccaagtttttttt---ttcttaacatgctagtgtaaatatgtttgcaggccgtcgtattacagtacattatactacctcagat
| |||||||||||||| ||| | ||||||   || ||||| || ||||| || |||||||||||||| || || ||| | |||||||| |||||||| ||||  ||  | |    | ||| |||  || | | |       | |  || | |  ||| | | ||    || | |    ||     |  | | ||      |   
AATATGATCCACGTCCGGTTAAGCCTGATAGCCTTTTTCCGGTGTTTTCTGTTACAAAGGGTATCACAGCAGGAATGATACATTGGCTGGTTGACAATGGgtatgttgtaacatgctatgaccatattgtctgtgcacctctgaactggttgcttaagt-tcttgtttggacatgaagtttt--catttcacacagaaaaaag-

upper sequence: LOC_Os06g48770.2 (Oryza sativa), 5'ss of exon 14
lower sequence: AT5G24810.2 (Arabidopsis thaliana), 5'ss of exon 15
AGTATGATCCACGTCCTGTTCAACCTGATTCTCTCTTTCCAGTTTTTTCAGTGACAAAGGGTATCACTGCTGGCATGGTGCATTGGCTTGTTGACAAAGGgtgagtg-------cttaatc------acaatgccaagtttttttttt-cttaacatgctagtgtaaatatgtttgcaggccgtcgtatt------acagtacattatactacctcagat-------------------------------------------------
  ||||| || ||||| |||||||| |||  | | ||||| ||||| || |||||||||||| |||||||||| ||| | |||||||||||||||||| |||||||         |||| |      | |||  || || ||  |||  |  | | || || | | |||  |  | ||  |   | ||||      |  ||  |||  |  | | ||  |                                                 
GATATGACCCTCGTCCAGTTCAACCCGATAGTTTATTTCCTGTTTTCTCTGTGACAAAGGGTGTCACTGCTGGAATGATACATTGGCTTGTTGACAAAAGgtgagtaacaacattttaagctttcaaaaaatttcatgtattcatttcacacaccctgatattttgaat-cggctccaatcttacatattggtctcattgttaattccatgatcccatttgcagaacacatgcttagtcatatttagtaatatttattcaatgatacag

upper sequence: LOC_Os06g48770.2 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv04s0008g02740.t01 (Vitis vinifera), 5'ss of exon 14
AGTATGATCCACGTCCTGTTCAACCTGATTCTCTCTTTCCAGTTTTTTCAGTGACAAAGGGTATCACTGCTGGCATGGTGCATTGGCTTGTTGACAAAGGgtgagtgctta--atcacaa-tgccaagttttttttttcttaa--catgctagtgtaaatatgtt--tgcaggccgtcgtattacagtacattatactacctcagat
  |||||||| ||||| ||||||||||||   || ||||| ||||| || || ||||||||||| || || || ||| | |||||||| |||||||||||||  ||  ||   || |  | |   ||  ||   | ||||| |  |     |||| || |  |||  |     ||  | |  | |    ||  ||   ||       
GATATGATCCTCGTCCAGTTCAACCTGATAGCCTATTTCCTGTTTTCTCCGTAACAAAGGGTATTACAGCAGGAATGATACATTGGCTGGTTGACAAAGGgtatgtaattgtgattatgactattaatgttgcatgttcttgaatccattcagtgcaattgcgttcctttccacctccatcctgccac-caacatggcaca------

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|58606319|gb|CK034352.1|CK034352
EST:     GTGACAAAGGGTATCACTGCTGGCATGGTGCATTGGCTTGTTGACAAAGG                         GAAGTTGAAGTATGAGGAGACTGTTGCCAATATATGGCCAAAATTCGGAAC
genomic: GTGACAAAGGGTATCACTGCTGGCATGGTGCATTGGCTTGTTGACAAAGGgtgagtgctt ... tatctttcagGAAGTTGAAGTATGAGGAGACTGTTGCCAATATATGGCCAAAATTCGGAAC
EST: gi|58590136|gb|CF988444.1|CF988444
EST:     GTGACAAAGGGTATCACTGCTGGCATGGTGCATTGGCTTGTTGACAAAGG                         GAAGTTGAAGTATGAGGAGACTGTTGCCAATATATGGCCAAAATTCGGAAC
genomic: GTGACAAAGGGTATCACTGCTGGCATGGTGCATTGGCTTGTTGACAAAGGgtgagtgctt ... tatctttcagGAAGTTGAAGTATGAGGAGACTGTTGCCAATATATGGCCAAAATTCGGAAC
EST: gi|87005733|gb|CI316152.1|CI316152
EST:     GTGACAAAGGGTATCACTGCTGGCATGGTGCATTGGCTTGTTGACAAAGG                         GAAGTTGAAGTATGAGGAGACTGTTGCCAATATATGGCCAAAATTCGGAAC
genomic: GTGACAAAGGGTATCACTGCTGGCATGGTGCATTGGCTTGTTGACAAAGGgtgagtgctt ... tatctttcagGAAGTTGAAGTATGAGGAGACTGTTGCCAATATATGGCCAAAATTCGGAAC
EST: gi|58605848|gb|CK033881.1|CK033881
EST:     GTGACAAAGGGTATCACTGCTGGCATGGTGCATTGGCTTGTTGACAAAGG                         GAAGTTGAAGTATGAGGAGACTGTTGCCAATATATGGCCAAAATTCGGAAC
genomic: GTGACAAAGGGTATCACTGCTGGCATGGTGCATTGGCTTGTTGACAAAGGgtgagtgctt ... tatctttcagGAAGTTGAAGTATGAGGAGACTGTTGCCAATATATGGCCAAAATTCGGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTATGATCCACGTCCTGTTCAACCTGATTCTCTCTTTCCAGTTTTTTCAGTGACAAAGGGTATCACTGCTGGCATGGTGCATTGGCTTGTTGACAAAGGgtgagtgcttaatcacaatgccaagttttttttttcttaacatgctagtgtaaatatgtttgcaggccgtcgtattacagtacattatactacctcagat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccgtcg