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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttagtcaagcatgccattaatggtttctttactctttcttaaaaaatcacatgttcaacatgttaactttgtgcaaccccagGTACTCCACAAATACACTGGTATATAATGACTAGCCCCTTTACTGATGAAGCGACTCGAAAATTTTTTGAAAGCCACAGATATTTTGGCTTAGAGCCTGA

Basic information

species Oryza sativa
transcript LOC_Os08g10600.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G155729_T01 (Zea mays), 3'ss of exon 5
gtaatttagtcaagcatgccattaatggtttctttactcttt-cttaaaaaatcacatgttcaaca-------tgttaactttgtgcaaccccagGTACTCCA---CAAATACACTGGTATATAATGACTAGCCCCTTTACTGATGAAGCGACTCGAAAATTTTTTGAAAGCCACAGATATTTTGGCTTAGAGCCTGA
||||  ||||           ||| | |||| ||||   ||   ||||  || ||    |||   |       | |||||| | |||| |||||||||   ||   ||||| ||||||||||||||||| || || ||||| ||||||| ||| ||||| || ||||||| ||||||||||||||| ||         
gtaaaatagttttaatcctttttactagtttatttatgtttgatttaattaaacattctttcgctaaaactgctcttaactatttgcagCCCCAGGTAGCACAGTGCAAATTCACTGGTATATAATGACGAGTCCTTTTACCGATGAAGTGACCCGAAAGTTCTTTGAAACCCACAGATATTTTGGTTT---------

upper sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 6
gtaatttagtcaagcatgccattaatggtttctttactctttc-ttaaaaaatcacatgttcaacatgttaactttgtgcaaccccagGTACTCCA---CAAATACACTGGTATATAATGACTAGCCCCTTTACTGATGAAGCGACTCGAAAATTTTTTGAAAGCCACAGATATTTTGGCTTAGAGCCTGA
        || |          |  |||||   || ||||  | |||     | | ||  |||  | ||| |  |  ||||    |   | || ||   |||||||||||||| || |||||||| || || |||||||| || || || ||||| |||||||| || | || ||||||  |         
--------gtaagtttcatttgtcttggttcagtttctctcgcattatttggttagatcctcatta-gtttatgtattgcagATTCTTCTTCTTCAGTGCAAATACACTGGTACATCATGACTAGTCCATTCACTGATGAGGCAACACGCAAATTCTTTGAAAGTCATAAATTTTTTGGTCT---------

upper sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G31070.2 (Arabidopsis thaliana), 3'ss of exon 5
----------------gtaatttagtcaagcatgccattaatggtttctttactctttcttaaaaaatcacatgttcaacatgttaactt-tgtgcaaccccagGTACTCCACA---AATACACTGGTATATAATGACTAGCCCCTTTACTGATGAAGCGACTCGAAAATTTTTTGAAAGCCACAGATATTTTGGCTTAGAGCCTGA
                 |   ||  || |   | | |   ||  ||       | |  | ||    |     | |||  |||  || |||  || ||   |||  |  ||||     |||||| |||||||| |||||||| || ||||||||||||||||| ||||||| |||    || ||||  || |||||  |         
gtgagtgagactactcatggcttcttctatattccaacagatatttgtaccgttatgccatatttgacactcttttccgcataatatcttacgttcagGTCCAATTCGTCCAGTTACAATACATTGGTATATTATGACTAGTCCATTTACTGATGAAGCGACACGAAAATATTTCTCGAGTCACAAGTACTTTGGTCT---------

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|218500747|gb|FG962718.1|FG962718
EST:     GCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGCATG                         GTACTCCACAAATACACTGGTATATAATGACTAGCCCCTTTACTGATGAA
genomic: GCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTG-ATGgtaatttagt ... gcaaccccagGTACTCCACAAATACACTGGTATATAATGACTAGCCCCTTTACTGATGAA
EST: gi|27576482|gb|CA999176.1|CA999176
EST:     AGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG                         GTACTCCACAAATACACTGGTATATAATGACTAGCCCCTTTACTGATGAAG
genomic: AGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATGgtaatttagt ... gcaaccccagGTACTCCACAAATACACTGGTATATAATGACTAGCCCCTTTACTGATGAAG
EST: gi|29616664|gb|CB621676.1|CB621676
EST:     AGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATG                         GTACTCCACAAATACACTGGTATATAATGACTAGCCCCTTTACTGATGAAG
genomic: AGCTGAACGAATTTTGTGCATACAGAAGCTGGCTGCTCAGTCCACTGATGgtaatttagt ... gcaaccccagGTACTCCACAAATACACTGGTATATAATGACTAGCCCCTTTACTGATGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactctttcttaaaaaatcacatgttcaacatgttaactttgtgcaaccccagGTACTCCACAAATACACTGGTATATAATGACTAGCCCCTTTACTGATGAAGCGACTCGAAAATTTTTTGAAAGCCACAGATATTTTGGCTTAGAGCCTGA
                                 tgttaac  putative branch site (score: 2)
     tctttcttaaaaaat  TA-rich tract