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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGGGAAGATGTTGTGGCTGAATTGAGCAGGGCTATGGAAAGGCAAGGGCTTGATATGAAAGTTACAGCTCTTgtaagtaaattcttggttcatgactctgttaaaattatttatcatctgaaactttcccatgcctgctactgctatatgctgatgggtaaatacattggca...

Basic information

species Oryza sativa
transcript LOC_Os01g53930.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53930.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G856653_T01 (Zea mays), 5'ss of exon 4
GTGGGGGAAGATGTTGTGGCTGAATTGAGCAGGGCTATGGAAAGGCAAGGGCTTGATATGAAAGTTACAGCTCTTgtaagtaaattc-ttggttcatgactctgttaaaattatttatcatctgaaactttcccatg---cctgctactgctatatgctgatgggtaaatacattggca------------------------------------------------------------------------------------------------
|| || ||||||||||||||||||||||| ||||| ||||||||||| || ||||||||||||||| ||||||| |||| ||||||  || |||||  | | | | | |   | |  |||  |  |    | | ||      ||| | |  | |||||     | |   | | |||                                                                                                   
GTTGGAGAAGATGTTGTGGCTGAATTGAGTAGGGCCATGGAAAGGCAGGGTCTTGATATGAAAGTTGCAGCTCTGgtaattaaattagtttgttcactatt-tatcatatgaagtactcacatagacacatactatagaatttgccatttatttatgccttctgatgt-tgctttgagtttcttgctatgttttatcttgacgtccagcaaaggcccattgaacatattagaagtaaatacaacatgttaactgataggtaacatttttttacag
















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|58590994|gb|CF989302.1|CF989302
EST:     TGAGCAGGGCTATGGAAAGGCAAGGGCTTGATATGAAAGTTACAGCTCTT                         GTTAATGACACTGTAGGCACATTGGCTGGCGGAAGATATGTTGATAATGAC
genomic: TGAGCAGGGCTATGGAAAGGCAAGGGCTTGATATGAAAGTTACAGCTCTTgtaagtaaat ... ttttgcccagGTTAATGACACTGTAGGCACATTGGCTGGCGGAAGATATGTTGATAATGAC
EST: gi|29641463|gb|CB646470.1|CB646470
EST:     TGAGCAGGGCTATGGAAAGGCAAGGGCTTGATATGAAAGTTACAGCTCTT                         GTTAATGACACTGTAGGCACATTGGCTGGCGGAAGATATGTTGATAATGAC
genomic: TGAGCAGGGCTATGGAAAGGCAAGGGCTTGATATGAAAGTTACAGCTCTTgtaagtaaat ... ttttgcccagGTTAATGACACTGTAGGCACATTGGCTGGCGGAAGATATGTTGATAATGAC
EST: gi|58664374|gb|CK053060.1|CK053060
EST:     TGAGCAGGGCTATGGAAAGGCAAGGGCTTGATATGAAAGTTACAGCTCTT                         GTTAATGACACTGTAGGCACATTGGCTGGCGGAAGATATGTTGATAATGAC
genomic: TGAGCAGGGCTATGGAAAGGCAAGGGCTTGATATGAAAGTTACAGCTCTTgtaagtaaat ... ttttgcccagGTTAATGACACTGTAGGCACATTGGCTGGCGGAAGATATGTTGATAATGAC
EST: gi|58663006|gb|CK051692.1|CK051692
EST:     GAGCAGGGCTATGGAACAGGCAAGGGCTTGATATGAAAGTTACAGCTCTT                         GTTAATGACACTGTAGGCACATTGGCTGGC
genomic: GAGCAGGGCTATGGAA-AGGCAAGGGCTTGATATGAAAGTTACAGCTCTTgtaagtaaat ... ttttgcccagGTTAATGACACTGTAGGCACATTGGCTGGC
EST: gi|58655773|gb|CK044453.1|CK044453
EST:     TGAGCAGGGCTATGGAAAGGCAAGGGCTTGATATGAAAGTTACAGCTCTT                         GTTAATGACACTGTAGGCACATTGGCTGGCGGAAGATATGTTGATAATGAC
genomic: TGAGCAGGGCTATGGAAAGGCAAGGGCTTGATATGAAAGTTACAGCTCTTgtaagtaaat ... ttttgcccagGTTAATGACACTGTAGGCACATTGGCTGGCGGAAGATATGTTGATAATGAC
EST: gi|58661416|gb|CK050096.1|CK050096
EST:     GAGCAGGGCTATGGAAAGGCAAGGGCTTGATATGAAAGTTACAGGGTCT-                         GTTAATGACACTGTAGGCACATTGGCTGGCGGAAGATATGTTGATAATGA
genomic: GAGCAGGGCTATGGAAAGGCAAGGGCTTGATATGAAAGTTACAGC-TCTTgtaagtaaat ... ttttgcccagGTTAATGACACTGTAGGCACATTGGCTGGCGGAAGATATGTTGATAATGA
EST: gi|2796819|gb|AA750113.1|AA750113
EST:     ATGAAAGTTACAGCTCTT                         GTTAATGACACTGTAGGCACATTGGCTGGCGGAAGATATGTTGATAATGAC
genomic: ATGAAAGTTACAGCTCTTgtaagtaaat ... ttttgcccagGTTAATGACACTGTAGGCACATTGGCTGGCGGAAGATATGTTGATAATGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGGGGAAGATGTTGTGGCTGAATTGAGCAGGGCTATGGAAAGGCAAGGGCTTGATATGAAAGTTACAGCTCTTgtaagtaaattcttggttcatgactctgttaaaattatttatcatctgaaactttcccatgcctgctactgctatatgctgatgggtaaatacattggca

- - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC