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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgacgccgcgcgcgcgcgacacgctacatccccgcatgattacagctagctgctaacgagttcgtgtgtatgtgtacatgtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGGAGCAGCGGTTGTGGCACTCGCACGCGCACGAGATCAAGGCGGGGTTGTG

Basic information

species Oryza sativa
transcript LOC_Os01g54520.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54520.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G043521_T01 (Zea mays), 3'ss of exon 1
gtgcg-acgccgcgcgcgcgcgacacgcta-catccccgcatgatt-----aca---gctagctgctaacgagttcg-tgtgtatgtgtacatgt------------gtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGGAGCAGCGGTTGTGGCACTCGCACGCGCACGAGATCAAGGCGGGGTTGTG
|||||  | ||| || | | |  |   ||  ||||  |   |||||      ||   |||  |  | ||  ||  |  ||  | |   |  || |            |  |||||| |||||||| ||||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| | ||  ||||
gtgcgtgcaccgtgcaccc-catcttactgtcatcttcaattgattctttggcatgtgctcacgcccaagaaggacactgcatctacatggatcttttcttttaactgcatgcagGCGTGGAGTACATCGTGTCGAGGAAGATCTTCGACTCGCTGCCGGCGGAGGAGCAGCGGCTGTGGCACTCGCACGCGCACGAGATCAAGTCAGGCCTGTG
















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|88304825|gb|CI671070.1|CI671070
EST:     CCTCCAGTGCGCCGTCTACGACGCCGANGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGG
EST: gi|218488839|gb|FG965943.1|FG965943
EST:     CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGACTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218488131|gb|FG951351.1|FG951351
EST:     CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218486355|gb|FG966145.1|FG966145
EST:     CCTCCAGTGCGCCGTCTACGACGCCGACGACCAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGATG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218482892|gb|FG964851.1|FG964851
EST:     CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218494988|gb|FG969744.1|FG969744
EST:     CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218497590|gb|FG963948.1|FG963948
EST:     CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218488590|gb|FG967101.1|FG967101
EST:     CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218502724|gb|FG947962.1|FG947962
EST:     CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218484284|gb|FG946807.1|FG946807
EST:     CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218482695|gb|FG967370.1|FG967370
EST:     ACTCCAGTGCGCCGTCTACGACGCCGACGACAAGCAGGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGC
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGC
EST: gi|218481032|gb|FG967550.1|FG967550
EST:     CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218483642|gb|FG955546.1|FG955546
EST:     CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218487782|gb|FG970667.1|FG970667
EST:     CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218492101|gb|FG950662.1|FG950662
EST:     TGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: TGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218495064|gb|FG965798.1|FG965798
EST:     CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218490274|gb|FG964409.1|FG964409
EST:     CCGACGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: CCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218502758|gb|FG964165.1|FG964165
EST:     CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
EST: gi|218482805|gb|FG967504.1|FG967504
EST:     CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCG                         GAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG
genomic: CCTCCAGTGCGCCGTCTACGACGCCGACGACAAGCACGCCCGCCTCATCGgtgcgacgcc ... gtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgattacagctagctgctaacgagttcgtgtgtatgtgtacatgtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGGAGCAGCGGTTGTGGCACTCGCACGCGCACGAGATCAAGGCGGGGTTGTG
                tgctaac  putative branch site (score: 1)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgacgccgcgcgcgcgcgacacgctacatccccgcatgattacagctagctgctaacgagttcgtgtgtatgtgtacatgtgtgtgcagGAGTGGAGTATATCGTGTCGCGGAAGATCTTCGACTCGCTGCCGGCGGAGGAGCAGCGGTTGTGGCACTCGCACGCGCACGAGATCAAGGCGGGGTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA