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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgcaaacaaatgaactgttcatcctttttaatgatcacattgctgattttagaccattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTG

Basic information

species Oryza sativa
transcript LOC_Os03g17980.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 6
gtatatgcaaacaa-atgaac--tgttcatcctttttaatgatcacattgctga-ttttagaccattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTG
||||   ||  ||   ||| |  | |   | | ||||  |||     || || | |||| ||  | ||| |||||||||||||||||||||||||| ||||||||||| ||  |||| || ||||||||| | || ||||| |||||||||||  ||
gtatggacatgcattgtgagccttatatgttccttttggtgacttgtttactaaatttttgaaaactttgtagGCAACTGTTGCATATTATTTACTATTGGACAATCGGTTTAGAGCAACTAGTGGCTATCTTGGGGCAGATTATCAAGAATCAATG
















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|58667418|gb|CK056104.1|CK056104
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|58662658|gb|CK051344.1|CK051344
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         T
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctag-
EST: gi|58662658|gb|CK051344.1|CK051344
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         T
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctag-
EST: gi|29672731|gb|CB669006.1|CB669006
EST:     CAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: CAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|29673828|gb|CB670103.1|CB670103
EST:     CTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: CTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|58666104|gb|CK054790.1|CK054790
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|29616520|gb|CB621532.1|CB621532
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|58674982|gb|CK063669.1|CK063669
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|218478287|gb|FG959067.1|FG959067
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTGTTGGACAATCGATTCCGAGCTACCAGT
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|29663427|gb|CB659702.1|CB659702
EST:     ATGGAAAGGACCATGTGTGTG-ATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|218493226|gb|FG956765.1|FG956765
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|218482816|gb|FG952976.1|FG952976
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCG
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCG
EST: gi|218482252|gb|FG960526.1|FG960526
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGA
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGA
EST: gi|29614996|gb|CB620009.1|CB620009
EST:     AAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: AAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|2317303|gb|C22357.1|C22357
EST:     GGAAAGGACCATGTGTGTGAATCTCTGGCGCAATAGACTGCAGAATGGAG                         GCAACTGTTGGCATATTATTTACTCTTGGGACAATCGATTCCGAGCTACC
genomic: GGAAAGGACCATGTGTGTGAATCTCTG-CGCAATAGACTGCAGAATG-AGgtatatgcaa ... cattttctagGCAACTGTTG-CATATTATTTACTCTTGG-ACAATCGATTCCGAGCTACC
EST: gi|218484843|gb|FG952392.1|FG952392
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaactgttcatcctttttaatgatcacattgctgattttagaccattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTG
                               tgctgat  putative branch site (score: 3)
                                            ccattttct  putative PPT
               tttttaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgcaaacaaatgaactgttcatcctttttaatgatcacattgctgattttagaccattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG