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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcacactatctgctatagctctcttatgaattacctggcataggttctgatatctcaaccatcaccagttgatcacacgctctttctatgtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA

Basic information

species Oryza sativa
transcript LOC_Os04g55940.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55940.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 11
ttcacactatc-tgctatagctctcttatgaattacctggcataggttctgatatctcaaccatcaccagttgatcacacgctctttctatgtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA
  |    |||| |  |||  |  |     ||  |   | | || | | ||||  |       ||  |            |  |     | | |   ||||||||||   ||||||||||||||||||||||||||||||| | ||||||||||||||||| ||||||||||| |||||||||||||||||||| |
gaccagttatcatcttatttcatttcagagatctgttttgtatggat-ctgagctgcatttgatatctgaccccatttgcaatgcacttgtttcatcacagGATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA

upper sequence: LOC_Os04g55940.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G040017_T01 (Zea mays), 3'ss of exon 10
ttcacactatctgctatagctctcttatgaattacctggcataggttctg---atatctcaaccatcaccagt---tgatcacacgctctttctatgtttc--cacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA
        | | | |||   |||  | | | ||  | |  || |||| ||     || | | | |      ||   ||| |    ||  | |   ||||||    ||||||||   ||||||||||||||||||||||||||||||| | ||||||||||||||||| ||||||||||| ||||| |||||||||||||| |
-------gaccagttatca-tcttgtttcatttcaccgagattggttttgtacgaatttgagctacatttggtatctgaccctgtgcaatgtacttgtttcgttgcagGATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAA
















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|86484481|gb|CI127114.1|CI127114
EST:     AAACAGCAACGCTCTTCATACCAGTACTAGTCGTGGCATTTATGCTACAG                         GATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
genomic: AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttatt ... gtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
EST: gi|88262940|gb|CI366566.1|CI366566
EST:     TCTTCATAACAGTACTACTCGT-GCATTTATGCTACAG                         GATGGT-TTGCGAACTACTTGAAA-GACTTATGCTGATCTTGTGTTATCTA
genomic: TCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttatt ... gtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
EST: gi|66923908|gb|CX110756.1|CX110756
EST:     AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAG                         GATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
genomic: AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttatt ... gtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
EST: gi|86832984|gb|CI333583.1|CI333583
EST:     TTTATGCTACAG                         GATGGTGGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCT
genomic: TTTATGCTACAGgtaggttatt ... gtttccacagGATGGT-GTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCT
EST: gi|86258579|gb|CI064932.1|CI064932
EST:     AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAG                         GATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
genomic: AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttatt ... gtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
EST: gi|33381504|gb|CF196847.1|CF196847
EST:     AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAG                         GATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
genomic: AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttatt ... gtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
EST: gi|58669001|gb|CK057687.1|CK057687
EST:     AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAG                         GATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA
genomic: AAACAGCAACGCTCTTCATAACAGTACTAGTCGTGGCATTTATGCTACAGgtaggttatt ... gtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgatatctcaaccatcaccagttgatcacacgctctttctatgtttccacagGATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA
                                   ctctttctatgtttcc  CT-rich tract
                                      tttctat  TA-rich tract