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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttgtttcttaacatttctgtggagtatatatacactatttgtaatggtggaagctatagaaaatttgaactatttatttttgatacactaatttcagGCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCG

Basic information

species Oryza sativa
transcript LOC_Os01g05070.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G037134_T04 (Zea mays), 3'ss of exon 5
tgcttgtttcttaacatttctgtggagtatatatacactatttgtaatg---gtggaagctatagaaaatttgaactatttatttttgatacactaatttcagGCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCG
   || |||   || || | |   |  || | |||   | |||||  |    ||||| |   ||||  || |||    | | | ||| ||    |  || ||||||| |||||||| ||||| |||||||| || |||||||||||||| |||||||||
--attatttaccaa-atgtttaaagtttaaacataacttttttgtggtatacgtggacggcctagatcatctgagaagtgtttgtttcatttcatctttacagGCAACCCAGGTCAGCAGAAAGCTAAGGTCTCAGAACTACCAAAATTTGGAAGACCG

upper sequence: LOC_Os01g05070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G011031_T01 (Zea mays), 3'ss of exon 5
tgcttgtttcttaacatttctgtggagtatatataca---ctatttgtaatg---gtggaagctatagaaaatttgaactatttatttttgatacactaatttcagGCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCG
      | | || | |    | |  | | | || |||   || |||||  |    ||||| |   ||||  || |||   || | | ||| ||    |  || |||||||||| ||||||||||| |||||||| || |||||||||||||| |||||||||
------tctttttataccattatcaaatgtttaaacataactttttgtggtatacgtggatggcttagatcatctgagaaatgtttgtttcatttcttctttacagGCAATCCTGGTCAACAGAAAGCTAAGGTCTCAGAACTACCAAAATTTGGAAGACCG
















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|27546786|gb|CA767261.2|CA767261
EST:     ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCG                         GCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAA
genomic: ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCGgtatgtattt ... ctaatttcagGCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAA
EST: gi|86496195|gb|CI138828.1|CI138828
EST:     GCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCG                         GCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAA
genomic: GCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCGgtatgtattt ... ctaatttcagGCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAA
EST: gi|88588825|gb|CI706667.1|CI706667
EST:     ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCG                         GCAATCCAGGTCAACAGAAGGCTAAGGTTCCTGAACTACCAAAATTCGGAA
genomic: ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCGgtatgtattt ... ctaatttcagGCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAA
EST: gi|58586280|gb|CF984588.1|CF984588
EST:     ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCG                         GCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAA
genomic: ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCGgtatgtattt ... ctaatttcagGCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAA
EST: gi|218478522|gb|FG957886.1|FG957886
EST:     ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCG                         GCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCANAATTCGGAA
genomic: ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCGgtatgtattt ... ctaatttcagGCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAA
EST: gi|58674474|gb|CK063161.1|CK063161
EST:     ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCG                         GCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAA
genomic: ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCGgtatgtattt ... ctaatttcagGCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAA
EST: gi|25803803|gb|CA759764.1|CA759764
EST:     ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATC-TTGCCG                         C
genomic: ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCGgtatgtattt ... ctaatttcag-
EST: gi|25803803|gb|CA759764.1|CA759764
EST:     ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATC-TTGCCG                         C
genomic: ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCGgtatgtattt ... ctaatttcag-
EST: gi|300215765|gb|HO088391.1|HO088391
EST:     ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCG                         GCAATCCAGGTCAACAAAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAA
genomic: ACTTCCAGATTTAGCAAGGATTTCTACAGATGGTCTTGTTATCTTTGCCGgtatgtattt ... ctaatttcagGCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAA
EST: gi|88262627|gb|CI366401.1|CI366401
EST:     TACAGATGGTCTTG-TATCTTGGCCG                         GCAATCCAGGTCAACAGGAAGGGTAAGGTTTGTGAAGCTACCAAAATTCGT
genomic: TACAGATGGTCTTGTTATCTTTGCCGgtatgtattt ... ctaatttcagGCAATCCAGGTCAACA-GAAGGCTAAGGTTTCTGAA-CTACCAAAATTCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggtggaagctatagaaaatttgaactatttatttttgatacactaatttcagGCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCG
                                           cactaat  putative branch site (score: 2)
                 aaaatttgaactattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttgtttcttaacatttctgtggagtatatatacactatttgtaatggtggaagctatagaaaatttgaactatttatttttgatacactaatttcagGCAATCCAGGTCAACAGAAGGCTAAGGTTTCTGAACTACCAAAATTCGGAAGACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA