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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtctgttttgtaattgaccttaactttgttaagtttactagccaaaatgtaactatgacacttcgttgtatttatgctgaattttgcctgttgttagGTGAATGAATCCCGGTTATCTGAAGACTTGGATCAAACATGGGAGGTCCTTGCAGAGCCAATACAGACA

Basic information

species Oryza sativa
transcript LOC_Os03g19930.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g19930.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G126430_T02 (Zea mays), 3'ss of exon 1
ttagtctgttttgtaattgaccttaactttgttaagtttactagccaaaatgtaactatga-cacttcgttgtatttatgctgaattttgcctgttgttagGTGAATGAATCCCGGTTATCTGAAGACTTGGATCAAACATGGGAGGTCCTTGCAGAGCCAATACAGACA
    || |   | |  |   | |||   |||    |     |       |||||| ||||| ||            |||||||||||  |    ||   ||||||||||||| || ||| |||||||| |||| ||||| |||||||||||||| |||||||||||||||
aatatcagacgtttgctcttctttactattgacctgaaacatgcattgtatgtaattatgatcaggctagaactactatgctgaattg-gtgcctttacagGTGAATGAATCACGTTTAGCTGAAGACCTGGAGCAAACTTGGGAGGTCCTTGCTGAGCCAATACAGACA

upper sequence: LOC_Os03g19930.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G895991_T01 (Zea mays), 3'ss of exon 8
ttagtctgttttgtaattgacct----taactttgttaagtttactagccaaaat----gtaactatga-cacttcgttgtatttatgctgaattt-tgcctgttgttagGTGAATGAATCCCGGTTATCTGAAGACTTGGATCAAACATGGGAGGTCCTTGCAGAGCCAATACAGACA
         |||   |||||||     |||||| ||||| |||  |   |    |    |||| ||||| ||          | |||||||||||  ||| | |    ||||||||||| | || ||| ||||||||||||| ||||| |||||||||||||| |||||||||||||||
--------ctttactattgacccgagataacttggttaatttttttgcacgcgttttaagtaattatgatcaggctagatcttctatgctgaattggtgcttat--acagGTGAATGAAGCGCGTTTAGCTGAAGACTTGGAGCAAACTTGGGAGGTCCTTGCTGAGCCAATACAGACA

upper sequence: LOC_Os03g19930.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G359070_T01 (Zea mays), 3'ss of exon 8
ttagtctgttttgtaattgaccttaactttgttaagtttactagccaaaatgtaactatga-cacttcgttgtatttatgctgaattttgcctgttgttagGTGAATGAATCCCGGTTATCTGAAGACTTGGATCAAACATGGGAGGTCCTTGCAGAGCCAATACAGACA
   ||| |   | |  |   | |||   |||    |     |       |||||| ||||| ||            |||||||||||  |    ||   || |||||||||| || ||| |||||||| |||| ||||| |||||||||||||| |||||||||||||||
aatgtcagacgtttgctcttctttactattgacctgaaacatgcgttgtatgtaattatgatcaggctagaactactatgctgaattg-gtgcctttacagTTGAATGAATCACGTTTAGCTGAAGACCTGGAGCAAACTTGGGAGGTCCTTGCTGAGCCAATACAGACA

upper sequence: LOC_Os03g19930.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G131828_T01 (Zea mays), 3'ss of exon 1
ttagtctgttttgtaattgaccttaactttgttaagtttactagccaaaatgtaactatga-cacttcgttgtatttatgctgaattttgcctgttgttagGTGAATGAATCCCGGTTATCTGAAGACTTGGATCAAACATGGGAGGTCCTTGCAGAGCCAATACAGACA
    || |   | |  |   | |||   |||          |       |||||| ||||| ||            |||||||||||  |    ||   ||||||||||||| |  ||| || ||||| |||| ||||| |||||||||||||| |||||||||||||||
aatatcagacgtttgctcttctttactattgacctaaaacatgcattgtatgtaattatgatcaggctagaactactatgctgaattg-gtgcctttacagGTGAATGAATCACATTTAGCTAAAGACCTGGAGCAAACTTGGGAGGTCCTTGCTGAGCCAATACAGACA

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|86525702|gb|CI165908.1|CI165908
EST:     GAGGAATCAATAAGGTTCAG                         GTGAATGAATCCCGGTTATCTGAAGACTTGGATCAAACCTGGGAGGTCCTT
genomic: GAGGAATCAATAAGGTTCAGgtaggtggcc ... ctgttgttagGTGAATGAATCCCGGTTATCTGAAGACTTGGATCAAACATGGGAGGTCCTT
EST: gi|86250841|gb|CI007704.1|CI007704
EST:     ATTCACTCTTGGCTTACAAAGCTACATTGCGAGGAATCAATAAGGTTCAG                         GTGAATGAATCCCGGTTATCTGAAGACTTGGATCAAACATGGGAGGTCCTT
genomic: ATTCACTCTTGGCTTACAAAGCTACATTGCGAGGAATCAATAAGGTTCAGgtaggtggcc ... ctgttgttagGTGAATGAATCCCGGTTATCTGAAGACTTGGATCAAACATGGGAGGTCCTT
EST: gi|33808748|gb|CF330259.1|CF330259
EST:     ATTCACTCTTGGCTTACAAAGCTACATTGCGAGGAATCAATAAGGTTCAG                         GTGAATGAATCCCGGTTATCTGAAGACTTGGATCAAACATGGGAGGTCCTT
genomic: ATTCACTCTTGGCTTACAAAGCTACATTGCGAGGAATCAATAAGGTTCAGgtaggtggcc ... ctgttgttagGTGAATGAATCCCGGTTATCTGAAGACTTGGATCAAACATGGGAGGTCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaatgtaactatgacacttcgttgtatttatgctgaattttgcctgttgttagGTGAATGAATCCCGGTTATCTGAAGACTTGGATCAAACATGGGAGGTCCTTGCAGAGCCAATACAGACA
    atgtaac  putative branch site (score: 3)
                                       ttttgcct  putative PPT
                       ttgtatttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagtctgttttgtaattgaccttaactttgttaagtttactagccaaaatgtaactatgacacttcgttgtatttatgctgaattttgcctgttgttagGTGAATGAATCCCGGTTATCTGAAGACTTGGATCAAACATGGGAGGTCCTTGCAGAGCCAATACAGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - tgttttg
- - - - - - - - - - - - - - - - - - - - - -gccaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa