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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgaacttctgaactaaacattgtgggtggtttttcctgaaacacctttgtagtaatagcatatttaatccttcaatatttttggcagGAGCTGAAAATGAAAAGGCTGGTATTGTAAATCAACAGAAGCTGGAAAAGAAATTTGGCCAATCTTCTGTTTTTGTCGCATCCACACTTCTTGAGAATGG

Basic information

species Oryza sativa
transcript LOC_Os07g24190.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G028353_T02 (Zea mays), 3'ss of exon 11
gta--cgtgaacttctgaactaaacattgtgggtggtttttcctgaaacacctttgtagtaatagcatatttaatccttcaatatttttggcagGAGCTGAAAATGAAAAGGCTGGTATTGTAAATCAACAGAAGCTGGAAAAGAAATTTGGCCAATCTTCTGTTTTTGTCGCATCCACACTTCTTGAGAATGG
|||   |||| |||   ||  ||||| |   | | || ||    |||||  |||  |  | || || ||| ||| | |      ||    | ||||||||| |||||||| |||||||||||||||||||| ||  | |||||||||||||| || |||||||| ||||   ||||||||||||| || |||||
gtaactgtgagctttcaaag-aaacacttcagttagtctt----gaaacttcttcattttgatcgcctatctaaccttgtgtggttccctgtagGAGCTGAGAATGAAAAAGCTGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGTCAGTCTTCTGTCTTTGCAACATCCACACTTCTCGAAAATGG

upper sequence: LOC_Os07g24190.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G025231_T02 (Zea mays), 3'ss of exon 11
gta--cgtgaacttctgaactaaacattgtgggtggtttttcctgaaacacctttgtagtaatagcatatttaatccttcaatatttttggcagGAGCTGAAAATGAAAAGGCTGGTATTGTAAATCAACAGAAGCTGGAAAAGAAATTTGGCCAATCTTCTGTTTTTGTCGCATCCACACTTCTTGAGAATGG
|||   |||| ||||  ||  ||||| | |         ||| ||||||   ||  | || || ||  || ||| | |      ||    | ||||||||| ||||||||||| ||||||||||||||||| ||  | ||||||||||||||||||||||||||||||||  ||||||||||||| ||||||||
gtaactgtgagcttccaaag-aaacactata--------ttcttgaaac---ttcattgtgattgccaatgtaaccttgtgcggttccctgtagGAGCTGAGAATGAAAAGGCCGGTATTGTAAATCAACAAAAATTAGAAAAGAAATTTGGCCAATCTTCTGTTTTTGTTACATCCACACTTCTCGAGAATGG
















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|29632757|gb|CB637766.1|CB637766
EST:     AAATCAATCCCCTGCATATGCACTTGGTGAAATTGAGGAGGGTGCTCCAG                         GAGCTGAAAATGAAAAGGCTGGTATTGTAAATCAACAGAAGCTGGAAAAGA
genomic: AAATCAATCCCCTGCATATGCACTTGGTGAAATTGAGGAGGGTGCTCCAGgtacgtgaac ... tttttggcagGAGCTGAAAATGAAAAGGCTGGTATTGTAAATCAACAGAAGCTGGAAAAGA
EST: gi|58607492|gb|CK035525.1|CK035525
EST:     AAATCAATCCCCTGCATATGCACTTGGTGAAATTGAGGAGGGTGCTCCAT                         GAGCTGAAAATGAAAAGGCTGGTATTGTCAAATCAACAGAAGCTGGAAAAG
genomic: AAATCAATCCCCTGCATATGCACTTGGTGAAATTGAGGAGGGTGCTCCAGgtacgtgaac ... tttttggcagGAGCTGAAAATGAAAAGGCTGGTATTGT-AAATCAACAGAAGCTGGAAAAG
EST: gi|29628005|gb|CB633016.1|CB633016
EST:     AAATCAATCCCCTGCATATGCACTTGGTGAAATTGAGGAGGGTGCTCCAG                         GAGCTGAAAATGAAAAGGCTGGTATTGTAAATCAACAGAAGCTGGAAAAGA
genomic: AAATCAATCCCCTGCATATGCACTTGGTGAAATTGAGGAGGGTGCTCCAGgtacgtgaac ... tttttggcagGAGCTGAAAATGAAAAGGCTGGTATTGTAAATCAACAGAAGCTGGAAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgaaacacctttgtagtaatagcatatttaatccttcaatatttttggcagGAGCTGAAAATGAAAAGGCTGGTATTGTAAATCAACAGAAGCTGGAAAAGAAATTTGGCCAATCTTCTGTTTTTGTCGCATCCACACTTCTTGAGAATGG
                             atttaat  putative branch site (score: 4)
                                           tattttt  putative PPT
                           atatttaatccttcaa  TA-rich tract