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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttttcttatgaggcccgaaagttttagtttatagttagctatatgatccacctttgttaatgcagtacaatgcaacatacatgttctatattttgcagGTATCACTACAACGTTGCAGATTCAAGGCTTGTACAACACATTGACAAAGGGAATGAAGATGGTCTGTTTATCAGTTGCATAACATCTTGCTCAAATCTG

Basic information

species Oryza sativa
transcript LOC_Os01g54100.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G095634_T01 (Zea mays), 3'ss of exon 4
gtactttttcttatgaggcccgaaagttttagtttatagttagctatatgatccacctttgttaatg---cagtacaatgcaacatacatgttctatattttgcagGTATCACTACAACGTTGCAGATTCAAGGCTTGTACAACACATTGACAAAGGGAATGAAGATGGTCTGTTTATCAGTTGCATAACATCTTGCTCAAATCTG
     |  |||||  ||  | ||||||||   |  || |||| |  ||  ||    ||||||   ||   ||    ||| ||||  |      ||   |  |||||||| |||||||| ||| ||||||||||  ||| ||| ||||| || ||||||||||  ||||| |||||||||||||||||||||||||| ||  |||| 
----gtactcttagaagaactgaaagtttagttaaattgttaac-gtaccatgtgtctttgtggctgagccaaagtaattcaacgaattca--ctgggtactgcagGTACCACTACAATGTTTCAGATTCAAGAGTTGGACAGCACATCGAAAAAGGGAATGCCGATGGACTGTTTATCAGTTGCATAACATCTTGTTCCGATCTA

upper sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 11
gtactttttcttatgaggcccgaaagttttagtttatagttagctatatgatccacctttgttaatgcagtacaatgcaacatacatgttct-atattttgcagGTATCACTACAACGTTGCAGATTCAAGGCTTGTACAACACATTGACAAAGGGAATGAAGATGGTCTGTTTATCAGTTGCATAACATCTTGCTCAAATCTG
                         |||||  | |    |||  ||  |  |   |    | |  |  | |   |      | |  | || | || || || |||||||| || || ||||| |||    |||| |  ||||||||||| ||||| |||||||||||| | ||||||||  |  |  | ||||| || ||||| 
-------------------------gttttcttctgatattaaataagtt-tttgcaagagattttaaaatgtcagagcctaaaggtattatcattttgtgtagGTATCATTATAATGTTGCTGATGTGCGGCTGGCCCAACACATTGATAAAGGAAATGAAGATGGTTTATTTATCAGCAGTGTGGCTTCTTGTTCTAATCTT

upper sequence: LOC_Os01g54100.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 11
gtactttttcttatgaggcccgaaagttttagtttatagttagctatatgatccacctttgttaatgcagtacaatgcaacatacatgttctatattttg---cagGTATCACTACAACGTTGCAGATTCAAGGCTTGTACAACACATTGACAAAGGGAATGAAGATGGTCTGTTTATCAGTTGCATAACATCTTGCTCAAATCTG
                         |||||  | |    |||  ||  |  |   |   || |  |  |  |      | | || | ||  ||| |||||    |||||||| || || ||||| |||    |||| |  ||||||||||| ||||| |||||||||||| | ||||||||  |  |  | ||||| || ||||| 
-------------------------gttttcttctgatattaaataagtt-tttgcaagtgatttta-aaaatgtcagagcctaaaggtattatcttttggtgtagGTATCATTATAATGTTGCTGATGTGCGGCTGGCCCAACACATTGATAAAGGAAATGAAGATGGTTTATTTATCAGCAGTGTGGCTTCTTGTTCTAATCTT

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|218496998|gb|FG950841.1|FG950841
EST:     GCAACACAGTGGATTAGTGTTTATAATGCCAGACGGCCTATGAAACAAAG                         GTATCACTACAACGTTGCAGATTCAAGGCTTGTACAACACATTGACCAAGG
genomic: GCAACACAGTGGATTAGTGTTTATAATGCCAGACGGCCTATGAAACAAAGgtactttttc ... tattttgcagGTATCACTACAACGTTGCAGATTCAAGGCTTGTACAACACATTGACAAAGG
EST: gi|38483008|gb|CF966810.1|CF966810
EST:     GCAACACAGTGGATTAGTGTTTATAATGCCAGACGGCCTATGAAACAAAG                         GTATCACTACAACGTTGCAGATTCAAGGCTTGTACAACACATTGACAAAGG
genomic: GCAACACAGTGGATTAGTGTTTATAATGCCAGACGGCCTATGAAACAAAGgtactttttc ... tattttgcagGTATCACTACAACGTTGCAGATTCAAGGCTTGTACAACACATTGACAAAGG
EST: gi|58688056|gb|CK076743.1|CK076743
EST:     GCAACACAGTGGATTAGTGTTTATAATGCCAGACGGCCTATGAAACAAAG                         GTATCACTACAACGTTGCAGATTCAAGGCTTGTACAACACATTGACAAAGG
genomic: GCAACACAGTGGATTAGTGTTTATAATGCCAGACGGCCTATGAAACAAAGgtactttttc ... tattttgcagGTATCACTACAACGTTGCAGATTCAAGGCTTGTACAACACATTGACAAAGG
EST: gi|163919775|gb|EG710337.1|EG710337
EST:     ATGAAACAAAG                         GTATCACTACAACGTTGCAGATTCAAGGCTTGTACAACACATTGACAAAGG
genomic: ATGAAACAAAGgtactttttc ... tattttgcagGTATCACTACAACGTTGCAGATTCAAGGCTTGTACAACACATTGACAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatccacctttgttaatgcagtacaatgcaacatacatgttctatattttgcagGTATCACTACAACGTTGCAGATTCAAGGCTTGTACAACACATTGACAAAGGGAATGAAGATGGTCTGTTTATCAGTTGCATAACATCTTGCTCAAATCTG
           tgttaat  putative branch site (score: 3)
                                     atgttctatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttttcttatgaggcccgaaagttttagtttatagttagctatatgatccacctttgttaatgcagtacaatgcaacatacatgttctatattttgcagGTATCACTACAACGTTGCAGATTCAAGGCTTGTACAACACATTGACAAAGGGAATGAAGATGGTCTGTTTATCAGTTGCATAACATCTTGCTCAAATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG