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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcagtatgatgattatgatcatgtcatattatcatgaaggagctaattttgacagagcgtccttaattcatatgtagtatatttgcatgtgcatttttttccttgtcatgtaaatcacttaatgctgatagcaataaattcttagGTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAAGGTGATTATGACACATTCGAGAGGACAAGGGAGGAGCACCTTAAGAACC

Basic information

species Oryza sativa
transcript LOC_Os02g58020.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 7
gtatgcagtatgatgattatgatcatgtcatattatcatgaaggagctaattttgacagagcgtccttaattcatatgtagtatatttgcatgtgcatttttttccttgtcatgtaaatcacttaatgctgatagcaataaattcttagGTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAAGGTGATTATGACACATTCGAGAGGACAAGGGAGGAGCACCTTAAGAACC
                 ||||| ||    |||| ||     |||||||||||  |||| |         |||   |  ||| | ||||   | | | | | |    |||   | || |     || |  ||| | |   || || |||||| |||||||| || ||||||||||||||   ||| |||||||||||||||||||| ||||||||||| |||||||||||||| |||||||||||||| |
----------------gtatgaacacccaatatcatttcataggagctaattg-gacaaa---------atttgcac-tagcacatttttcttttcttgtgtggatttgaagtttatagtggatatt--tgacaacctgaactttttagGTTGTCACCGATATCCTTCATCTGCATGGTAGAAAACTACATGCTTACAAAGGTGACTATGACACATTTGAGAGGACAAGGGAAGAGCACCTTAAGAATC
















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|218482666|gb|FG970229.1|FG970229
EST:     GGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATACG                         GTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAA
genomic: GGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATACGgtatgcagta ... aaattcttagGTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAA
EST: gi|29662747|gb|CB659022.1|CB659022
EST:     GGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATACG                         GTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAA
genomic: GGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATACGgtatgcagta ... aaattcttagGTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAA
EST: gi|29644366|gb|CB649373.1|CB649373
EST:     GGCCAAAGACATTCATTGTTGTATCACATGCTANGGAGTTTCTTAATACG                         GTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACA
genomic: GGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATACGgtatgcagta ... aaattcttagGTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACA
EST: gi|24468674|gb|CA305623.1|CA305623
EST:     GGCCAAAGACATTCATTGTTGCATCACATGCTAGGGAGTTTCTTAATACG                         GTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAA
genomic: GGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATACGgtatgcagta ... aaattcttagGTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAA
EST: gi|218483226|gb|FG956166.1|FG956166
EST:     GGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATACG                         GTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAA
genomic: GGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATACGgtatgcagta ... aaattcttagGTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAA
EST: gi|86909957|gb|CI292894.1|CI292894
EST:     TGTATCACATGCTAGGGAGTTTCTTAATACG                         GTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAA
genomic: TGTATCACATGCTAGGGAGTTTCTTAATACGgtatgcagta ... aaattcttagGTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAA
EST: gi|58602069|gb|CK012597.1|CK012597
EST:     GGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATACG                         GTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAA
genomic: GGCCAAAGACATTCATTGTTGTATCACATGCTAGGGAGTTTCTTAATACGgtatgcagta ... aaattcttagGTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatttttttccttgtcatgtaaatcacttaatgctgatagcaataaattcttagGTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAAGGTGATTATGACACATTCGAGAGGACAAGGGAGGAGCACCTTAAGAACC
                                tgctgat  putative branch site (score: 3)
                                                ttctt  putative PPT
                                          aataaattctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcagtatgatgattatgatcatgtcatattatcatgaaggagctaattttgacagagcgtccttaattcatatgtagtatatttgcatgtgcatttttttccttgtcatgtaaatcacttaatgctgatagcaataaattcttagGTCGTCACCGACATTCTTCATCTGCATGGACAAAAGCTACATGCTTACAAAGGTGATTATGACACATTCGAGAGGACAAGGGAGGAGCACCTTAAGAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC