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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaccgtgtgactatctgtaaacaccatcagtccattgaaaaggaaaaacttttaatcctcacagctatttttgactttgctcccatttgttgtatgcagTTCATTGAAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGCCTGTCATATCTGATGAATGACAAGGCAGAACAAGCTCTCAGTGATGCGA

Basic information

species Oryza sativa
transcript LOC_Os04g58750.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58750.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 10
ggaccgtgtgactat-ctgtaaacaccatcagtccattgaaaaggaaaaactt--ttaatcctcacagctatttttgactttgctc-ccatttgttgt-atgcagTTCATTGAAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGCCTGTCATATCTGATGAATGACAAGGCAGAACAAGCTCTCAGTGATGCGA
     |  | | ||  ||  ||| | |     |  |      |      | ||   | |      | ||| | |  | |||| ||     ||  || | |||||||| |||||||||||||| |||||||| || ||||||||||| || ||||||||||||||||||||||||| || | || |  | ||  | | |||||| |
-----ggttaaatacgctaaaaatatcgctgttagaacaggcaaattgcagttacctgaaggctgctgctttctcggtcttttctaattgttctttatcatgcagTTTATTGAAGTTGGTACAATGGTTTCCCCAACCATTTATGCTCGACGTTGCCTGTCATATCTGATGAATGGCATGCCACAGGAGGCATTGAATGATGCAA
















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|88720188|gb|CI743487.1|CI743487
EST:     ATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTGACTGTTATTCTCAG                         TTCATTGAAGTTGGTACGATGGTTT
genomic: ATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTGACTGTTATTCTCAGgttgattttg ... ttgtatgcagTTCATTGAAGTTGGTACGATGGTTT
EST: gi|86482095|gb|CI124728.1|CI124728
EST:     ATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTGACTGTTATTCTCAG                         TTCATTGGAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGC
genomic: ATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTGACTGTTATTCTCAGgttgattttg ... ttgtatgcagTTCATTGAAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGC
EST: gi|33796952|gb|CF324339.1|CF324339
EST:     ATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTGACTGTTATTCTCAG                         TTCATTGAAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGC
genomic: ATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTGACTGTTATTCTCAGgttgattttg ... ttgtatgcagTTCATTGAAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGC
EST: gi|33675770|gb|CF304009.1|CF304009
EST:     ATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTGACTGTTATTCTCAG                         TTCATTGAAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGC
genomic: ATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTGACTGTTATTCTCAGgttgattttg ... ttgtatgcagTTCATTGAAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGC
EST: gi|29636566|gb|CB641575.1|CB641575
EST:     ATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTGACTGTTATTCTCAG                         TTCATTGAAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGC
genomic: ATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTGACTGTTATTCTCAGgttgattttg ... ttgtatgcagTTCATTGAAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGC
EST: gi|87005460|gb|CI285682.1|CI285682
EST:     ATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTGACTGTTATTCTCAG                         TTCATTGAAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGC
genomic: ATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTGACTGTTATTCTCAGgttgattttg ... ttgtatgcagTTCATTGAAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGC
EST: gi|33679197|gb|CF307436.1|CF307436
EST:     ATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTGACTGTTATTCTCAG                         TTCATTGAAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGC
genomic: ATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTGACTGTTATTCTCAGgttgattttg ... ttgtatgcagTTCATTGAAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaacttttaatcctcacagctatttttgactttgctcccatttgttgtatgcagTTCATTGAAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGCCTGTCATATCTGATGAATGACAAGGCAGAACAAGCTCTCAGTGATGCGA
                     tatttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaccgtgtgactatctgtaaacaccatcagtccattgaaaaggaaaaacttttaatcctcacagctatttttgactttgctcccatttgttgtatgcagTTCATTGAAGTTGGTACGATGGTTTCTCCGACCATTTATGCGCGGCGTTGCCTGTCATATCTGATGAATGACAAGGCAGAACAAGCTCTCAGTGATGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT