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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttcttaattcttccttcctgtttgctgaaattttgatatgcgatgatgttctgacttctggtcatcatatggaactctttagGCTACAGAGAGGTTTGAAGCAGCCTACCCAACAATCAAGGAGTTGGCCCTTGCTGGTCCTCCTGGCTCAAAAACCGTGAAACAAGCAGCACAGCAGCTTT

Basic information

species Oryza sativa
transcript LOC_Os01g03760.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g03760.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G155709_T02 (Zea mays), 3'ss of exon 6
gtttgttcttaattcttccttcctgtttgctgaaattttgatatgcgatgatgttctgacttctggtcatcatatggaactctttagGCTACAGAGAGGTTTGAAGCAGCCTACCCAACAATCAAGGAGTTGGCCCTTGCTGGTCCTCCTGGCTCAAAAACCGTGAAACAAGCAGCACAGCAGCTTT
        || |||  || | ||||    |     | ||  ||  |  |  ||        |||| | | |  | | || ||| ||||||||||| |||||||||| ||| || | |||||||||||||||||| ||||| ||| |||||||||| ||||| |||||||||||| ||||||| ||||
-------gtttatttctcatccctgagatcc----tcttagtaaacattcgtgagtcatgctctgatgacctaaagcaattctgtagGCTACAGAAAGGTTTGAAGTAGCTTATCGAACAATCAAGGAGTTGGCTCTTGCCGGTTCTCCTGGCTCTAAAACTGTGAAACAAGCATCACAGCAACTTT

upper sequence: LOC_Os01g03760.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G121683_T01 (Zea mays), 3'ss of exon 6
gtttgttcttaattcttccttcctgtttgctgaaattttgatatgcgatgatgttctgacttctggtcatcatatggaactctttagGCTACAGAGAGGTTTGAAGCAGCCTACCCAACAATCAAGGAGTTGGCCCTTGCTGGTCCTCCTGGCTCAAAAACCGTGAAACAAGCAGCACAGCAGCTTT
    |||| |  || |||||||||     ||    | ||  ||  |  | |||        |||| | | |  |   || ||| ||||||||||| |||||||||||||||||||||| ||||||||||||||| ||||| |||||||||||||||||||| |||||||||||| |||| |||||||
----gttcatt-tttttccttcctaagctct----tgttagtaaacattcatgagtcatgctctgatgacctaaaacaattctgtagGCTACAGAAAGGTTTGAAGCAGCCTACCCAATAATCAAGGAGTTGGCTCTTGCCGGTCCTCCTGGCTCAAAAACTGTGAAACAAGCATCACAACAGCTTT
















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|325493777|gb|JG458301.1|JG458301
EST:     GATCTGTTCATGAGAGCTGCATTTCCTGTTTCCAGCACTCGTGTAAAG                         GCTACAGAGAGGTTTGAAGCAGCCTACCCAACAATCAAGGAGTTGGCCCTT
genomic: GATCTGTTCATGAGAGCTGCATTTCCTGTTTCCAGCGCTCGTGTAAAGgtttgttctt ... aactctttagGCTACAGAGAGGTTTGAAGCAGCCTACCCAACAATCAAGGAGTTGGCCCTT
EST: gi|29645275|gb|CB650282.1|CB650282
EST:     TTGATCTGTTCATGAGAGCTGCATTTCCTGTTTCCAGCGCTCGTGTAAAG                         GCTACAGAGAGGTTTGAAGCAGCCTA
genomic: TTGATCTGTTCATGAGAGCTGCATTTCCTGTTTCCAGCGCTCGTGTAAAGgtttgttctt ... aactctttagGCTACAGAGAGGTTTGAAGCAGCCTA
EST: gi|40493511|gb|BX900802.1|BX900802
EST:     TTGATCTGTTCATGAGAGCTGCATTTCCTGTTTCCAGCGCTCGTGTAAAG                         GCTACAGAGAGGTTTGAAGCAGCCTACCCAACAATCAAGGAGTTGGCCCTT
genomic: TTGATCTGTTCATGAGAGCTGCATTTCCTGTTTCCAGCGCTCGTGTAAAGgtttgttctt ... aactctttagGCTACAGAGAGGTTTGAAGCAGCCTACCCAACAATCAAGGAGTTGGCCCTT
EST: gi|27548128|gb|CA766270.2|CA766270
EST:     TTGATCTGTTCATGAGAGCTGCATTTCCTGTTTCCAGCGCTCGTGTAAAG                         GCTACAGAGAGGTTTGAAGCAGCCTACCCAACAATCAAGGAGTTGGCCCTT
genomic: TTGATCTGTTCATGAGAGCTGCATTTCCTGTTTCCAGCGCTCGTGTAAAGgtttgttctt ... aactctttagGCTACAGAGAGGTTTGAAGCAGCCTACCCAACAATCAAGGAGTTGGCCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattttgatatgcgatgatgttctgacttctggtcatcatatggaactctttagGCTACAGAGAGGTTTGAAGCAGCCTACCCAACAATCAAGGAGTTGGCCCTTGCTGGTCCTCCTGGCTCAAAAACCGTGAAACAAGCAGCACAGCAGCTTT
                     ttctgac  putative branch site (score: 2)
                                               ctcttt  putative PPT
     ttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttcttaattcttccttcctgtttgctgaaattttgatatgcgatgatgttctgacttctggtcatcatatggaactctttagGCTACAGAGAGGTTTGAAGCAGCCTACCCAACAATCAAGGAGTTGGCCCTTGCTGGTCCTCCTGGCTCAAAAACCGTGAAACAAGCAGCACAGCAGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT