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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttgcctactatattatatgccatcacagccaggagatttatactgatgtataatacaatagcctttacagaatattaataactaatatctcttgtagGTTCTCGAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAG

Basic information

species Oryza sativa
transcript LOC_Os12g01140.4
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01140.3 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G001457_T02 (Zea mays), 3'ss of exon 11
tatttgcctactatattatatgccatcacagccaggagatttatactgatgtataatacaatagcctttacagaatatt--aataactaata------tctcttgtagGTTCTCGAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAG
              ||| ||||||     |    ||| ||   ||   | | | ||||  | | | || | | |        ||| || ||       | |||| |||||||| ||||  |||||||| |||| ||| |||||||| || |||||||  || |||||||||||||| ||||| ||
---nnnnnnnnnnnattgtatgcc----taatttggaaatcactagacaagca-aatattacatctttcaaaaatctcctagatagctcatgcaattttttcttatagGTTCTTGAGAACGGTGAAAGCATTGATTTGAAACATTTCAGACCAGTAAGGCCTTTAGGATCTGGTGATACTGGCAG

upper sequence: LOC_Os11g01140.3 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 12
----------------------------tatttgc-ctactatattatatg----ccatcacagccaggagatttatactgatgtataatacaatagcct-----ttacagaatattaataactaat--atct-----------------cttgtagGTTCTCGAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAG
                            || ||   | |||  ||| |       |  |    | |  ||  ||| || |    ||| ||||  ||   |       |||   | |   ||||| ||  || |                  ||| || |||| ||   ||| |||   || ||  | ||||| ||||||||||||||||| || ||||||||||||||||| ||
gtactgtggctagataaatataacatgctacttataccacttcattctgcattccctgttgtggtcctgaattttttattttattattatactttaatttaataccaacatgctttctttaactcattcatttgtttgggaaacccctgatttgcagATTCTAGAAGATGGAGAACAGATAGGCCTGAAACACTTTAGGCCAGTAAAACCGTTGGGATCTGGTGACACTGGCAG
















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|29622723|gb|CB627734.1|CB627734
EST:     TGCCAAATCCACATATGAAAGATACTGCATCATGGAGAGCCATCCAAAAG                         GTTCTCGAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAA
genomic: TGCCAAATCCACATATGAAGGATACTGCATCATGGAGAGCCATCCAAAAGgtatgatttg ... tctcttgtagGTTCTCGAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAA
EST: gi|29672018|gb|CB668293.1|CB668293
EST:     TGCCAAATCCACATATGAAGGATACTGCATCATGGAGAGCCATCCAAAAG                         GTTCTCTAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAA
genomic: TGCCAAATCCACATATGAAGGATACTGCATCATGGAGAGCCATCCAAAAGgtatgatttg ... tctcttgtagGTTCTCGAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAA
EST: gi|29613611|gb|CB618624.1|CB618624
EST:     TGCCAAATCCACATATGAAAGATACTGCATCATGGAGAGCCATCCAAAAG                         GTTCTCGAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAA
genomic: TGCCAAATCCACATATGAAGGATACTGCATCATGGAGAGCCATCCAAAAGgtatgatttg ... tctcttgtagGTTCTCGAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAA
EST: gi|29627346|gb|CB632357.1|CB632357
EST:     TGCCAAATCCACATATGAAAGATACTGCATCATGGAGAGCCATCCAAAAG                         -TTCTCGAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAA
genomic: TGCCAAATCCACATATGAAGGATACTGCATCATGGAGAGCCATCCAAAAGgtatgatttg ... tctcttgtagGTTCTCGAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAA
EST: gi|29641400|gb|CB646407.1|CB646407
EST:     TGCCAAATCCACATATGAAGGATACTGCATCATGGAGAGCCATCCAAAAG                         GTTCTCGAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAA
genomic: TGCCAAATCCACATATGAAGGATACTGCATCATGGAGAGCCATCCAAAAGgtatgatttg ... tctcttgtagGTTCTCGAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatgtataatacaatagcctttacagaatattaataactaatatctcttgtagGTTCTCGAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAG
                                           tatctctt  CT-rich tract
                     tttacagaatattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttgcctactatattatatgccatcacagccaggagatttatactgatgtataatacaatagcctttacagaatattaataactaatatctcttgtagGTTCTCGAGAGTGGTGAAAGTATTGGTTTAAAACATTTTAGGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG