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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatatcattttaaagggtttgccctctgcatagacaccatacaaatattctctgtgccagtgactaatttttgccaataccttactgtgtattttttagGGAACAAGATCAATGGATTCAATGTGATGATTGCTCAAAATGGCGCCGGTTACCACTTAATGTTATTGTTGCATCCAAGTGGACATGTGCTGACAACACA

Basic information

species Oryza sativa
transcript LOC_Os07g48200.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 9
tgatatcattttaaagggtttgccctctgcatagacaccatacaaatattctctgtgccagtgactaatttttgccaa-taccttactgtgtattttttagGGAACAAGATCAATGGATTCAATGTGATGATTGCTCAAAATGGCGCCGGTTACCACTTAATGTTATTGTTGCATCCAAGTGGACATGTGCTGACAACACA
| || | || |||||||| ||| || || ||| | |||| | ||| ||| | ||| || ||| | || | | ||||||| | ||||||||||| || |||||||||||||| || |||||||||||||||||||| || ||||||||||||||||||||||| |||||||| | |||||| ||
cgtcatactgtttgagggtttgttgtctaaatggaagtcatgtacatatcgttggtgtcagcgtgccgtttatgtcaaatttctgattttgtatttgt-agGGAACAAGACCAGTGGATTCAATGTGACGAGTGCTCAAAATGGCGCCGGTTGCCTCTTAATGTTATTGTTGCATCCAAATGGACATGCACCGACAACTCA

upper sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G172621_T01 (Zea mays), 3'ss of exon 9
tgatatcattttaaagggtttgccctctgcatagacac-catacaaatatt-----ctctgtgccagtg-actaatttttgccaataccttactgtgtattttttagGGAACAAGATCAATGGATTCAATGTGATGATTGCTCAAAATGGCGCCGGTTACCACTTAATGTTATTGTTGCATCCAAGTGGACATGTGCTGACAACACA
| || || ||| || | |||| ||| || |||| || ||||| | |||| | | ||| | || | ||||||| | |||||||||||||| |||||||||||||| || |||||||||||||||||||| || ||||||||||||||||| |||| |||||||| | |||||| ||
------taaattgaaaaagttgtccaaagttgtgacattcattcatctattggcgacttgacatcagtgtgccaattatgtcaaatttcctattttgtatttgt-agGGAACAAGATCAGTGGATTCAATGTGACGACTGCTCAAAATGGCGCCGGTTGCCTCTTAATGTTATTGTTGCGCCCAAATGGACATGCACCGACAACTCA
















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|29689253|gb|CB685528.1|CB685528
EST:     GAGATCAA-TTTT-CCTATCCGTTCTACTGG                         GGAACAAGATCAATGGATTCAATGTGATGATTGCTCAAAATGGCGCCGGTT
genomic: GAGATCAATTTTTACC-ATCCGTTCTACTGGgtaagaacct ... tattttttagGGAACAAGATCAATGGATTCAATGTGATGATTGCTCAAAATGGCGCCGGTT
EST: gi|38469181|gb|CF953312.1|CF953312
EST:     GAACCCCCTGTGTTTGCAAAGAGATCAATTTTTACCATCCGTTCTACTGG                         GGAACAAGATCAATGGATTCAATGTGATGATTGCTCAAAATGGCGCCGGTT
genomic: GAACCCCCTGTGTTTGCAAAGAGATCAATTTTTACCATCCGTTCTACTGGgtaagaacct ... tattttttagGGAACAAGATCAATGGATTCAATGTGATGATTGCTCAAAATGGCGCCGGTT
EST: gi|58689987|gb|CK078674.1|CK078674
EST:     GAACCCCCTGTGTTTGCAAAGAGATCAATTTTTACCATCCGTTCTACTGG                         GGAACAAGATCAATGGATTCAATGTGATGATTGCTCAAAAGGGCGCCGGTT
genomic: GAACCCCCTGTGTTTGCAAAGAGATCAATTTTTACCATCCGTTCTACTGGgtaagaacct ... tattttttagGGAACAAGATCAATGGATTCAATGTGATGATTGCTCAAAATGGCGCCGGTT
EST: gi|51946086|gb|CV152427.1|CV152427
EST:     GAACCCCCTGTGTTTGCAAAGAGATCAATTTTTACCATCCGTTCTACTGG                         GGAACAAGATCAATGGATTCAATGTGATGATTGCTCAAAATGGCGCCGGTT
genomic: GAACCCCCTGTGTTTGCAAAGAGATCAATTTTTACCATCCGTTCTACTGGgtaagaacct ... tattttttagGGAACAAGATCAATGGATTCAATGTGATGATTGCTCAAAATGGCGCCGGTT
EST: gi|58686025|gb|CK074712.1|CK074712
EST:     GAACCCCCTGTGTTTGCAAAGAGATCAATTTTTACCATCCGTTCTACTGG                         GGAACAAGATCAATGGATTCAATGTGATGATTGCTCAAAATGGCGCCGGTT
genomic: GAACCCCCTGTGTTTGCAAAGAGATCAATTTTTACCATCCGTTCTACTGGgtaagaacct ... tattttttagGGAACAAGATCAATGGATTCAATGTGATGATTGCTCAAAATGGCGCCGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattctctgtgccagtgactaatttttgccaataccttactgtgtattttttagGGAACAAGATCAATGGATTCAATGTGATGATTGCTCAAAATGGCGCCGGTTACCACTTAATGTTATTGTTGCATCCAAGTGGACATGTGCTGACAACACA
                                             tatttttt  CT-rich tract
 tgtatttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatatcattttaaagggtttgccctctgcatagacaccatacaaatattctctgtgccagtgactaatttttgccaataccttactgtgtattttttagGGAACAAGATCAATGGATTCAATGTGATGATTGCTCAAAATGGCGCCGGTTACCACTTAATGTTATTGTTGCATCCAAGTGGACATGTGCTGACAACACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - ctctgca
- - - - - - - - - - - - - - - - - - -ccataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - gtgccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttactg