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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAGgttagttatgacacatgagtcttgtttcttacatgtttgatttatatattgttatatgaaccccatgtttttttgtccagttgcttatgtaagtactaac...

Basic information

species Oryza sativa
transcript LOC_Os03g63020.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63020.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G045241_T07 (Zea mays), 5'ss of exon 7
ATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAGgttagttatgacacatgagtcttgtttctt---acatg---tttgatttatatattg-ttatatgaaccccatgttt--ttttgtccagttgctt------atgtaagtactaac--------------------------------------------
|  || ||||||||  ||||||||||||||||||||||| | |  ||||| ||||| ||||| |||||     |  | || ||  |||    | ||   |||||   | |  | ||  || |  ||  |        ||| |   | | |    |||||||      || |  | | | ||                                            
AATCCTCCAAGAAACTTATGGGAGCTTATTCCTAATGCTTCATCTGAAGCAATCGATTTGATCCAGgtacaccaatagac-tgcttctatgctgttgggacatgatatctattctaagtactaatttcacactttttatgctacatctagctttgttgctttacatgatttgcgcaatgacagttctcaatattaacatggtaccattctgcttctttttgttag

upper sequence: LOC_Os03g63020.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA03G21610.1 (Glycine max), 5'ss of exon 11
ATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAGgttagttatgacacatgagtcttgtttcttacatgtttgatttatatattgttatatgaaccccatgttttt--ttgtccagttgcttatgtaagtactaac---------------
 | || ||    || || |   |  ||||||| ||||||| |||||||||||| ||||||||    ||  | | | |   ||    | | |||||  |    |  ||  | | |    |  |   |    |  |  |   | || || |    ||  ||   |||                  
GTTCCGCCTGTGAAGCTTTCTAATATTATTCCGAATGCTAGTTTGGAAGCTATAGACTTGATCACAgtatgctttaatcaattgaacctctttctctctctatgcatacacacacacatgcagacattgtaaatactaaatagtgcaatcttcta-atatccactgcttcgtaaaatccgtag
















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|29644979|gb|CB649986.1|CB649986
EST:     ATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAG                         CAACTTTGTTCCTGGGATCCACGAAGAAGGCCAACTGCTGAGCAATCACTA
genomic: ATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAGgttagttatg ... attctgacagCAACTTTGTTCCTGGGATCCACGAAGAAGGCCAACTGCTGAGCAATCACTA
EST: gi|29613120|gb|CB618133.1|CB618133
EST:     ATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAG                         CAACTTTGTTCCTGGGATCCACGAAGAAGGCCAACTGCTGAGCAATCACTA
genomic: ATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAGgttagttatg ... attctgacagCAACTTTGTTCCTGGGATCCACGAAGAAGGCCAACTGCTGAGCAATCACTA
EST: gi|29666009|gb|CB662284.1|CB662284
EST:     ACTTGATTCAG                         CAACTTTGTTCCTGGGATCCACGAAAGAAGGCCAACTGCTGAGCAATCACT
genomic: ACTTGATTCAGgttagttatg ... attctgacagCAACTTTGTTCCTGGGATCCACG-AAGAAGGCCAACTGCTGAGCAATCACT
EST: gi|58675001|gb|CK063688.1|CK063688
EST:     TATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAG                         CAACTTTGTTCCTGGGATCCACGAA
genomic: TATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAGgttagttatg ... attctgacagCAACTTTGTTCCTGGGATCCACGAA
EST: gi|34996388|gb|CF569133.1|CF569133
EST:     TATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAG                         CAACTTTGTTCCTGGGATCCACGAAGAAGGCCAACTGCTGAGCAATCACTA
genomic: TATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAGgttagttatg ... attctgacagCAACTTTGTTCCTGGGATCCACGAAGAAGGCCAACTGCTGAGCAATCACTA
EST: gi|29666008|gb|CB662283.1|CB662283
EST:     ACTTGATTCAG                         CAAC-TTGTTCCTGGGATCCACGAAGAAGGCCAACTGCTGAGCAATCACTA
genomic: ACTTGATTCAGgttagttatg ... attctgacagCAACTTTGTTCCTGGGATCCACGAAGAAGGCCAACTGCTGAGCAATCACTA
EST: gi|218497584|gb|FG955131.1|FG955131
EST:     ATCGACTTGATTCAG                         CAACTTTGTTCCTGGGATCCACGAAGAAGGCCAACTGCTGAGCAATCACTA
genomic: ATCGACTTGATTCAGgttagttatg ... attctgacagCAACTTTGTTCCTGGGATCCACGAAGAAGGCCAACTGCTGAGCAATCACTA
EST: gi|33381171|gb|CF196514.1|CF196514
EST:     TATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAG                         CAACTTTGTTC
genomic: TATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAGgttagttatg ... attctgacagCAACTTTGTTC
EST: gi|33381337|gb|CF196680.1|CF196680
EST:     TATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAG                         CAACTTTGTTCCTGGGATCCACGAAGAAGGCCAACTGCTGAGCAATCACTA
genomic: TATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAGgttagttatg ... attctgacagCAACTTTGTTCCTGGGATCCACGAAGAAGGCCAACTGCTGAGCAATCACTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCCCACCAAGAAATCTATGGGAGCTTATTCCTAATGCTACTTTGGAAGCTATCGACTTGATTCAGgttagttatgacacatgagtcttgtttcttacatgtttgatttatatattgttatatgaaccccatgtttttttgtccagttgcttatgtaagtactaac

- - - - - - - - - - GGAGCT
- - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - -  TGGAAG