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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATGACGAAAAGAGAATATGTAGAAGATCAAGATGCTGAAGATCCTGATGACTTCATCATCTCACTAACAACTCAGgtattgttctcttttagttttgtttaattttgataccttgttgagcatatttcctaatctgatatatcccacgcaaactgggaggatgtctcaggaaact...

Basic information

species Oryza sativa
transcript LOC_Os08g22864.2
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g22864.2 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G327394_T01 (Zea mays), 5'ss of exon 21
GAAATGACGAAAAGAGAATATGTAGAAGATCAAGATGCTGAAGATCCTGATGACTTCATCATCTCACTAACAACTCAGgtat-tgttctcttttagttttgtttaattttgataccttgttgagcatatt--tcctaatctgatatatcccacgcaaactgggaggatgtctcaggaaact
|||||||| ||||||||||| || |||||||||||||||||||||||||||||||| || ||||| || ||||||||||||   |  |  |    ||||  ||| |||||     |      |    |||  |  ||| ||  |   ||| | | |||| |                    
GAAATGACCAAAAGAGAATACGTCGAAGATCAAGATGCTGAAGATCCTGATGACTTTATTATCTCCCTTACAACTCAGgtacgcgaccaataaatgtttctttttattttagctgccaacatattgaattaatggtaaacttgttcttccaatgtaaacag--------------------
















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|86480174|gb|CI122807.1|CI122807
EST:     TCATCTCACTAACAACTCAG                         ATCGCACGTAGGGATGAAGAAATGGCTCCTTATATTGCAGAATCTAAAAGG
genomic: TCATCTCACTAACAACTCAGgtattgttct ... atctgaacagATCGCACGTAGGGATGAAGAAATGGCTCCTTATATTGCAGAATCTAAAAGG
EST: gi|58586846|gb|CF985154.1|CF985154
EST:     ATCAAGATGCTGAAGAT-CTGATGATTTCATCATCTCACTAACAACTCAG                         ATCGCGCGTAGGGATGAAGAAATGGCTCCTTATATTGCAGAATCTAAAAGG
genomic: ATCAAGATGCTGAAGATCCTGATGACTTCATCATCTCACTAACAACTCAGgtattgttct ... atctgaacagATCGCACGTAGGGATGAAGAAATGGCTCCTTATATTGCAGAATCTAAAAGG
EST: gi|29624113|gb|CB629124.1|CB629124
EST:     ATCAAGATGCTGAAGATCCTGATGACTTCATCATCTCACTAACAACTCAG                         ATCGCACGGAGGGATGAAGAAATGGCTCCTTATATTGCAGAATCTAAAAGG
genomic: ATCAAGATGCTGAAGATCCTGATGACTTCATCATCTCACTAACAACTCAGgtattgttct ... atctgaacagATCGCACGTAGGGATGAAGAAATGGCTCCTTATATTGCAGAATCTAAAAGG
EST: gi|29626007|gb|CB631018.1|CB631018
EST:     ATCAAGATGCTGAAGATCCTGATGACTTCATCATCTCACTAACAACTCAG                         ATCGCACGGAGGGATGAAGAAATGGCTCCTTATATTGCAGAATCTAAAAGG
genomic: ATCAAGATGCTGAAGATCCTGATGACTTCATCATCTCACTAACAACTCAGgtattgttct ... atctgaacagATCGCACGTAGGGATGAAGAAATGGCTCCTTATATTGCAGAATCTAAAAGG
EST: gi|88670678|gb|CI724794.1|CI724794
EST:     ATCAAGATGCTGAAGATCCTGATGACTTCATCATCTCACTAACAACTCAG                         ATCGCACGTAGGGATGAAGAAATGGCTCCTTATATTGCAGAATCTAAAAGG
genomic: ATCAAGATGCTGAAGATCCTGATGACTTCATCATCTCACTAACAACTCAGgtattgttct ... atctgaacagATCGCACGTAGGGATGAAGAAATGGCTCCTTATATTGCAGAATCTAAAAGG
EST: gi|88671305|gb|CI724351.1|CI724351
EST:     ATCAAGATGCTGAAGATCCTGATGACTTCATCATCTCACTAACAACTCAG                         ATCGCACGTAGGGATGAAGAAATGGCTCCTTATATTGCAGAATCTAAAAGG
genomic: ATCAAGATGCTGAAGATCCTGATGACTTCATCATCTCACTAACAACTCAGgtattgttct ... atctgaacagATCGCACGTAGGGATGAAGAAATGGCTCCTTATATTGCAGAATCTAAAAGG
EST: gi|58692351|gb|CK081038.1|CK081038
EST:     ATCAAGATGCTGAAGATCCTGATGATTTCATCATCTCACTAACAACTCAG                         ATCGCACGTAGGGATGAAGAAATGGCTCCTTATATTGCAGAATCTAAAAGG
genomic: ATCAAGATGCTGAAGATCCTGATGACTTCATCATCTCACTAACAACTCAGgtattgttct ... atctgaacagATCGCACGTAGGGATGAAGAAATGGCTCCTTATATTGCAGAATCTAAAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATGACGAAAAGAGAATATGTAGAAGATCAAGATGCTGAAGATCCTGATGACTTCATCATCTCACTAACAACTCAGgtattgttctcttttagttttgtttaattttgataccttgttgagcatatttcctaatctgatatatcccacgcaaactgggaggatgtctcaggaaact

- - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - TGAAGA