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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgaaaccaataatgtatgtgaaatcttatctgctgtaaaatcatcatagaaatttgtgtttctgatcccatgaaatggtcttgtggatatatatgcagATATGGAACACAGAGTGAAGTGCATGCTCTTACTCCTTGGAGAGGAAGCTGATTCCTTTTCAAAAAGGGCAGAGATGTACTACAAAAGGCGGCCGGAGGT

Basic information

species Oryza sativa
transcript LOC_Os01g74510.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g74510.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G438704_T01 (Zea mays), 3'ss of exon 1
tatgaaaccaataatgtatgtgaaatcttatctgctgtaaaatcatcatagaaatttgtgtttctgatcccatgaaatggtcttgtggatatatatgcagATATGGAACACAGAGTGAAGTGCATGCTCTTACTCCTTGGAGAGGAAGCTGATTCCTTTTCAAAAAGGGCAGAGATGTACTACAAAAGGCGGCCGGAGGT
                                    ||||    || ||  |    ||  |||       |      || | | ||   |  ||  ||||||||||||||||| ||||||||||||||||| |||||||| ||||| ||||||||||| || || |||||||||||||||||||| ||||| || |||||
------------------------------------gtaatga-atgattcatgcatgatttttaatgtgcgctgtgtgat-tcgtccttgaattcgcagATATGGAACACAGGGTGAAGTGCATGCTCTTGCTCCTTGGGGAGGAGGCTGATTCCTTCTCGAAGAGGGCAGAGATGTACTACAAGAGGCGACCTGAGGT

upper sequence: LOC_Os01g74510.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G062587_T01 (Zea mays), 3'ss of exon 1
tatgaaaccaataatgtatgtgaaatcttatctgctgtaaaatcatcatagaaatttgtgtttctgatcccatgaaa-----tggtcttgtggatatatatgcagATATGGAACACAGAGTGAAGTGCATGCTCTTACTCCTTGGAGAGGAAGCTGATTCCTTTTCAAAAAGGGCAGAGATGTACTACAAAAGGCGGCCGGAGGT
     ||  |   || |||    |    ||| |      | ||    ||| | || | ||||| ||  || |  |||     |  ||||| | |  ||| |||||||||||||||||| || |||||||||||||| |||||||| ||||| || |||||||| ||||| |||||||||||||||||||| ||||| || |||||
----taattatatatatatacatatatatatatatatatatatatatatatatatatatgtttttgcacctaacaaaacaactaatcttg-gtacttatttgcagATATGGAACACAGGGTCAAGTGCATGCTCTTGCTCCTTGGGGAGGAGGCCGATTCCTTCTCAAAGAGGGCAGAGATGTACTACAAGAGGCGACCTGAGGT
















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|88722804|gb|CI746314.1|CI746314
EST:     GAGCCACATCCGCACCAAGCAGTCCAAATGGCTTGATAGCCATCTCCAAG                         ATATGGAACACAGAGTGAAGTGCATGCTCTTACTCCTTGGAGAGGAAGCTG
genomic: GAGCCACATCCGCACCAAGCAGTCCAAATGGCTTGATAGCCATCTCCAAGgtgaccgtcc ... atatatgcagATATGGAACACAGAGTGAAGTGCATGCTCTTACTCCTTGGAGAGGAAGCTG
EST: gi|88398670|gb|CI598635.1|CI598635
EST:     GAGCCACATCCGCACCAAGCAGTCCAAATGGCTTGATAGCCATCTCCAAG                         ATATGGAACACAGAGTGAAGTGCATGCTCTTACTCCTTGGAGAGGAAGCTG
genomic: GAGCCACATCCGCACCAAGCAGTCCAAATGGCTTGATAGCCATCTCCAAGgtgaccgtcc ... atatatgcagATATGGAACACAGAGTGAAGTGCATGCTCTTACTCCTTGGAGAGGAAGCTG
EST: gi|88724481|gb|CI747740.1|CI747740
EST:     GAGCCACATCCGCACCAAGCAGTCCAAATGGCTTGATAGCCATCTCCAAG                         ATATGGAACACAGAGTGAAGTGCATGCTCTTACTCCTTGGAGAGGAAGCTG
genomic: GAGCCACATCCGCACCAAGCAGTCCAAATGGCTTGATAGCCATCTCCAAGgtgaccgtcc ... atatatgcagATATGGAACACAGAGTGAAGTGCATGCTCTTACTCCTTGGAGAGGAAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatagaaatttgtgtttctgatcccatgaaatggtcttgtggatatatatgcagATATGGAACACAGAGTGAAGTGCATGCTCTTACTCCTTGGAGAGGAAGCTGATTCCTTTTCAAAAAGGGCAGAGATGTACTACAAAAGGCGGCCGGAGGT
                ttctgat  putative branch site (score: 3)
                                           atatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgaaaccaataatgtatgtgaaatcttatctgctgtaaaatcatcatagaaatttgtgtttctgatcccatgaaatggtcttgtggatatatatgcagATATGGAACACAGAGTGAAGTGCATGCTCTTACTCCTTGGAGAGGAAGCTGATTCCTTTTCAAAAAGGGCAGAGATGTACTACAAAAGGCGGCCGGAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - aaaccaa
- - - - - - -atgtatg
- - - - - - - - - - - - - - - tctgctg
- - - - - - - - - - - - - - - - - - - - - - - catagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcccatg