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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGATCAAAGATAAGGAGAATGTGACTCTTGAGGACGTGTTACAGCCTGGAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacctcctaatccatcctactctataaatgtcataattctcacctgaatataacctgtgtaactaatttgatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g64660.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64660.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G836250_T02 (Zea mays), 5'ss of exon 5
CATGATCAAAGATAAGGAGAATGTGACTCTTGAGGACGTGTTACAGCCTGGAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacctcctaatcc-----atcctac--tctataaatgtcataattctcacctgaatataacc----tgtgtaactaatttgatgcag
||| ||||| || ||||| || || ||||| ||||||||| | || ||||| || |||||| | || || |||||||||||||||||||||||||||||||||||  |||   |||| |     | || |   |||   || || || ||    | |  |||||||      || | ||| ||| ||||||||
CATCATCAAGGACAAGGACAACGTCACTCTGGAGGACGTGCTGCAACCTGGCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaat-aaccaattaattctcttgaacccatcttctccgaaggtaatcatctgtaacgaaatataattgacatgcgcaaccaatctgatgcag
















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|29686739|gb|CB683014.1|CB683014
EST:     GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|38473796|gb|CF957928.1|CF957928
EST:     NAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|58588683|gb|CF986991.1|CF986991
EST:     GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|58590217|gb|CF988525.1|CF988525
EST:     GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|29613014|gb|CB618027.1|CB618027
EST:     GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|38480766|gb|CF964855.1|CF964855
EST:     GAAAAAACATGGGTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|29617760|gb|CB622772.1|CB622772
EST:     CTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: CTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|33820806|gb|CF336207.1|CF336207
EST:     G-AAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|4714676|gb|AU055793.1|AU055793
EST:     GAAAAAACATGGTTGCNGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|27546650|gb|CA764792.2|CA764792
EST:     GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTCGATCCATCT
genomic: GAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
EST: gi|29682614|gb|CB678889.1|CB678889
EST:     ATACTGCATGTACGGCAGTTCCTGCACG                         CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT
genomic: ATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacc ... tttgatgcagCTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGATCAAAGATAAGGAGAATGTGACTCTTGAGGACGTGTTACAGCCTGGAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacctcctaatccatcctactctataaatgtcataattctcacctgaatataacctgtgtaactaatttgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA