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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatctcgaatgagttgtgtcatcaccacattttatcagtttgatctttgtacaactcgagacatgccaaactcttcactgtattgatgacatgctgcagGCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCCTTGATGCATCTCGAAAAAGAGCTACCTGGATCTTGTGAGGTGCTGATTG

Basic information

species Oryza sativa
transcript LOC_Os07g32400.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g32400.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G027756_T01 (Zea mays), 3'ss of exon 17
caat-ctcgaatgagttgtgtcatcaccacattttatcagtttgatctttgtacaactcgagacatg----ccaaactcttcactgtattgatgacatgctgcagGCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCCTTGATGCATCTCGAAAAAGAGCTACCTGGATCTTGTGAGGTGCTGATTG
 | | ||  | ||     |   | ||    || || |  | ||  || ||| |   |||  ||||||    ||||  | |  ||  ||||| |  |||| || |||||||||||||||||||| |  | || | ||||||| | |||||||||||||||||| || | |||   ||  |||||||||| || || || ||| |||
-agtgcttaagtgttcattcagaccagtcaatctttt--gctt--tcattgcatccctccggacatgtcttccaacttttggacattattgctttcatgatgtagGCTACTGGTGACAAGTTTGATCGGCCTGCTGTTCATGCCTTCCTTGATTCCTTGATGGATTTAGAACGTGATATACCTGGATCATGCGAAGTACTGGTTG
















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|88228909|gb|CI226760.1|CI226760
EST:     CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAG                         GCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCC
genomic: CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAGgtacagtata ... catgctgcagGCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCC
EST: gi|33678909|gb|CF307148.1|CF307148
EST:     CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAG                         GCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCC
genomic: CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAGgtacagtata ... catgctgcagGCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCC
EST: gi|88236841|gb|CI234692.1|CI234692
EST:     CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAG                         GCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCC
genomic: CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAGgtacagtata ... catgctgcagGCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCC
EST: gi|88273108|gb|CI388564.1|CI388564
EST:     CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAG                         GCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCC
genomic: CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAGgtacagtata ... catgctgcagGCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCC
EST: gi|86528838|gb|CI169044.1|CI169044
EST:     CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAG                         GCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCC
genomic: CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAGgtacagtata ... catgctgcagGCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCC
EST: gi|86844981|gb|CI340969.1|CI340969
EST:     CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAG                         GCTACTGGTGACAAGTTTAACGGACCAGTTGTTCAAACATTCCTTGATTCC
genomic: CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAGgtacagtata ... catgctgcagGCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCC
EST: gi|87032664|gb|CI270299.1|CI270299
EST:     CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAG                         GCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCC
genomic: CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAGgtacagtata ... catgctgcagGCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCC
EST: gi|87020794|gb|CI269511.1|CI269511
EST:     CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAG                         GCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCC
genomic: CTGTATCTTCACCTGCACTCTCGTCATTGATAATTCCTTCTCTAAAAGAGgtacagtata ... catgctgcagGCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgtacaactcgagacatgccaaactcttcactgtattgatgacatgctgcagGCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCCTTGATGCATCTCGAAAAAGAGCTACCTGGATCTTGTGAGGTGCTGATTG
                                    tattgat  putative branch site (score: 3)
                                    tattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatctcgaatgagttgtgtcatcaccacattttatcagtttgatctttgtacaactcgagacatgccaaactcttcactgtattgatgacatgctgcagGCTACTGGTGACAAGTTTAACGGACCAGTTGTTCATACATTCCTTGATTCCTTGATGCATCTCGAAAAAGAGCTACCTGGATCTTGTGAGGTGCTGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT