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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaaatgcttccaaataggattctatgccacattttctgtggactgaattacttatgtaatctgaaaggctggttgacactgataaaaaaaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCTGCTGTTGTTACACTTGCTGTGTGAGGAGAAAGCTTCGTCAAAAGCTAAA

Basic information

species Oryza sativa
transcript LOC_Os03g06120.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g06120.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G027821_T01 (Zea mays), 3'ss of exon 5
tcaaaatgcttccaaataggattctatgccacattttctgtggactga----attacttatgtaatctgaaaggctggttgacactga---taaaaaaaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCTGCTGTTGTTACACTTGCTGTGTGAGGAGAAAGCTTCGTCAAAAGCTAAA
    | |    | || ||  |  | || |  | |||   || || ||     |  |||| ||| | || |||| ||  ||  ||| |    |         ||||||| ||   ||| || ||||||||||||||||| || ||||| ||||| |||||||| ||||| || |||||||| ||||||||||||||||||||| |  |
----attaaagcaaagtaaaa--ccatacatcctttcaagtagaatgctgtcacaacttttgtgagct-aaagccttctttgcacggtatctctgtgttgttttcagCTTCTGGGGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCTGCTGCTGTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGA
















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|25806375|gb|CA762336.1|CA762336
EST:     CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT                         TATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
genomic: CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
EST: gi|87021652|gb|CI276051.1|CI276051
EST:     CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT                         CATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
genomic: CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
EST: gi|58681562|gb|CK070249.1|CK070249
EST:     CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT                         CATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
genomic: CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
EST: gi|88961682|gb|CI096900.1|CI096900
EST:     AAGATTGCTTCAATTGCGAAGAACAGGCCCATGT                         TATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
genomic: AAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
EST: gi|58673353|gb|CK062039.1|CK062039
EST:     CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT                         CATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGA
genomic: CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGA
EST: gi|88961463|gb|CI096770.1|CI096770
EST:     TTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT                         CATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
genomic: TTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
EST: gi|44674180|gb|CR287614.1|CR287614
EST:     CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT                         CATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
genomic: CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
EST: gi|29637808|gb|CB642817.1|CB642817
EST:     CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT                         CATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
genomic: CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
EST: gi|33803496|gb|CF327623.1|CF327623
EST:     CAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT                         CATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCA
genomic: CAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
EST: gi|89169017|gb|CI020557.1|CI020557
EST:     CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT                         CATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
genomic: CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
EST: gi|33803494|gb|CF327622.1|CF327622
EST:     CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT                         CATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATAT-ATCCA
genomic: CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
EST: gi|88962482|gb|CI097634.1|CI097634
EST:     TGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT                         CATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
genomic: TGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
EST: gi|27548516|gb|CA766467.2|CA766467
EST:     CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT                         CATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
genomic: CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
EST: gi|58596859|gb|CK007387.1|CK007387
EST:     CTGGGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT                         CATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
genomic: CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
EST: gi|87034567|gb|CI189191.1|CI189191
EST:     CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT                         CATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
genomic: CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
EST: gi|86886085|gb|CI321121.1|CI321121
EST:     GAACAGGCCCATGT                         CATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
genomic: GAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
EST: gi|88906222|gb|CI375294.1|CI375294
EST:     CTGTGGAACATTCTCAAAGATTGCTTCAATGGCGAAGAACAGGCCCATGT                         CATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT
genomic: CTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGTgtaagaatat ... aaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattacttatgtaatctgaaaggctggttgacactgataaaaaaaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCTGCTGTTGTTACACTTGCTGTGTGAGGAGAAAGCTTCGTCAAAAGCTAAA
                                 cactgat  putative branch site (score: 3)
                                  actgataaaaaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaaatgcttccaaataggattctatgccacattttctgtggactgaattacttatgtaatctgaaaggctggttgacactgataaaaaaaaatttcagCATCGTCGGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCTGCTGTTGTTACACTTGCTGTGTGAGGAGAAAGCTTCGTCAAAAGCTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA