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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacagctatcactgatatttttttctcccttatcttgttgttggagttgctgcttctaggcgctcacttgtttgctcaaacttccttctcttcttaatgctgagaagcatgaatctttcacatattcactaaaagccactgattttgcccacttgttttacaatttagtatatttttctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAGTCTGATGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTT

Basic information

species Oryza sativa
transcript LOC_Os10g11140.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g11140.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G025854_T01 (Zea mays), 3'ss of exon 20
gtacacagctatcactgatatttttttctcccttatcttgttgttggagttgctgcttctaggcgctcacttgtttgctcaaacttccttctcttcttaatgc-tgagaagcatgaatctttcacatattcactaaaagccactgat-tttgcccacttgttttacaatttagtatatttttctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAGTCTGATGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTT
                                                                                                    | | |  |  || |   |   | | | ||  | |||||     |||  ||||  |        ||  ||| |||||      ||| |  |||||||||||||||||||||| || |||||  | ||||| || ||||| || ||||||  ||| ||||||  ||| ||||| |||| ||||||||||||||
---------------------------------------------------------------------------------------------------gtacatctgttgcttcgtttcctgaaaaatata-taaaaattgttgacgtttgatctaaaacaatatgattaagtatg-----ctcctgcagGGAACCGGATCTGCTGGAGCTACTATCCGCCTCTACATAGAACAATTTGAATCTGATATCTCGAAGCATAGTCTCGATGCTCAAACAGCTTTGAAGCCTT

upper sequence: LOC_Os10g11140.1 (Oryza sativa), 3'ss of exon 20
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 20
gtacacagctatcactgatatttttttctcccttatcttgttgttggagttgctgcttctaggcgctcacttgtttgctcaaacttccttctcttcttaatgctgagaagcatgaatctttcacatattcactaaaagccactgattttgcccacttgttttacaatttagtatatttttctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAGTCTGATGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTT
                                                                        || || |  |  ||| |||| || ||  |  | |  |   |  || ||| | || |  |   | |  || ||        |||  ||     || ||||   | || | | ||  ||||||| || || |||||||| ||| | || ||||||||||| ||||| ||| | || |  ||||| |||||| ||||||||||||||||| | || ||||
------------------------------------------------------------------------gtatgttgtagattctttctttttttctt--taatcaaattccatgttttatatgt--atagagacacattggcccctatcaca-gtgaactaacttag---aattctttgttccagGGAACTGGCTCAGCTGGAGCTACAGTGCGAATATACATTGAACAATTTGAGCCAGACGTTTCAAAACATGATGTGGATGCACAAATAGCTCTTAAACCTT
















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|89198777|gb|CI003514.1|CI003514
EST:     GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG                         GGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
genomic: GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
EST: gi|24468665|gb|CA305614.1|CA305614
EST:     GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG                         GGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
genomic: GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
EST: gi|24468739|gb|CA305688.1|CA305688
EST:     GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG                         GGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
genomic: GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
EST: gi|88849912|gb|CI001618.1|CI001618
EST:     GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG                         GGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
genomic: GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
EST: gi|44665107|gb|CR278541.1|CR278541
EST:     GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG                         GGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
genomic: GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
EST: gi|86892654|gb|CI312043.1|CI312043
EST:     GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG                         GGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
genomic: GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
EST: gi|88531137|gb|CI459588.1|CI459588
EST:     GGCTTCGA-TTGTATTCACCGATGGATCTAGGATTATCTTCCCCCTTTCG                         GGAACCGGATCTGCTGGAGCCACAATCCGTATATACATTGAGCAATTCGAG
genomic: GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
EST: gi|88966651|gb|CI365874.1|CI365874
EST:     GGCTTCGA-TTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCT                         GGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGACCAATTCGAG
genomic: GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
EST: gi|86257302|gb|CI004120.1|CI004120
EST:     GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG                         GGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
genomic: GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
EST: gi|58611262|gb|CK038974.1|CK038974
EST:     GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG                         GGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
genomic: GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
EST: gi|86842613|gb|CI341764.1|CI341764
EST:     GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG                         GGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
genomic: GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
EST: gi|44665085|gb|CR278519.1|CR278519
EST:     GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG                         GGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
genomic: GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
EST: gi|86503671|gb|CI146304.1|CI146304
EST:     GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG                         GGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
genomic: GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
EST: gi|29681951|gb|CB678226.1|CB678226
EST:     GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG                         GGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
genomic: GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
EST: gi|88544375|gb|CI473075.1|CI473075
EST:     TGTATTCAGCGATGGATCTAGGATTATCTTCCCCCTTTCG                         GGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
genomic: TGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
EST: gi|86498572|gb|CI141205.1|CI141205
EST:     GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCG                         GGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG
genomic: GGCTTCGATTTGTATTCACCGATGGATCTAGGATTATCTTCCGCCTTTCGgtacacagct ... tctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagccactgattttgcccacttgttttacaatttagtatatttttctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAGTCTGATGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTT
                                     tatatttttctctt  CT-rich tract
                        ttttacaatttagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacagctatcactgatatttttttctcccttatcttgttgttggagttgctgcttctaggcgctcacttgtttgctcaaacttccttctcttcttaatgctgagaagcatgaatctttcacatattcactaaaagccactgattttgcccacttgttttacaatttagtatatttttctcttatagGGAACCGGATCTGCTGGAGCAACAATCCGTATATACATTGAGCAATTCGAGTCTGATGCCTCAAAGCATGATCTGGATGCACAAATAGCTTTGAAGCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC