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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcatttatcgacactttatgatactgtgatttggaatagtctgtaatatttatgtgaataattcattatggcagGTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTGATGCTTGGTATTCTGATGGTCATGGTTCAGTAGAAAGCACTGCTGCATA

Basic information

species Oryza sativa
transcript LOC_Os11g42420.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g42420.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G348675_T02 (Zea mays), 3'ss of exon 21
gtatcatttatcgacactttatgatactgtgatttggaatagtctgtaatatttatgtgaataattcattatggcagGTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTGATGCTTGGTATTCTGATGGTCATGGTTCAGTAGAAAGCACTGCTGCATA
||| | ||| |           || ||     |||| |||| |  ||    | | | | ||| ||   |||||||||||||||||| ||| || |||||||||||||| || | ||| ||||||||||||||||||||||||||  |   |||||| || || ||||| ||||| ||
gtacc-ttttttattctaaagggagaccactgtttgaaatatttcgtgcggtgtttttaaatgatctgttatggcagGTGAACTCAGTCGGTTCCAACCTGGAGTTTCGATGGCAATTTCACGGCTTGATGCTTGGTATTCTGACCGGAGTGGTTCCGTGGAGAGCACCGCTGCTTA
















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|58679628|gb|CK068315.1|CK068315
EST:     TATGGCTGCTGGGTTCAAAG                         GTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTG
genomic: TATGGCTGCTGGGTTCAAAGgtatcattta ... attatggcagGTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTG
EST: gi|58665324|gb|CK054010.1|CK054010
EST:     AGCCAATGATGGAGGTCTTCTTGCTGCAATTATGGCTGCTGGGTTCAAAG                         GTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTG
genomic: AGCCAATGATGGAGGTCTTCTTGCTGCAATTATGGCTGCTGGGTTCAAAGgtatcattta ... attatggcagGTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTG
EST: gi|58693556|gb|CK082243.1|CK082243
EST:     AGCCAATGATGGAGGTCTTCTTGCTGCAATTATGGCTGCTGGGTTCAAAG                         GTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTG
genomic: AGCCAATGATGGAGGTCTTCTTGCTGCAATTATGGCTGCTGGGTTCAAAGgtatcattta ... attatggcagGTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTG
EST: gi|29629130|gb|CB634141.1|CB634141
EST:     AGCCAATGATGGAGGTCTTCTTGCTGCAATTATGGCTGCTGGGTTCAAAG                         GTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTG
genomic: AGCCAATGATGGAGGTCTTCTTGCTGCAATTATGGCTGCTGGGTTCAAAGgtatcattta ... attatggcagGTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTG
EST: gi|29627724|gb|CB632735.1|CB632735
EST:     AGCCAATGATGGAGGTCTTCTTGCTGCAATTATGGCTGCTGGGTTCAAAG                         GTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTG
genomic: AGCCAATGATGGAGGTCTTCTTGCTGCAATTATGGCTGCTGGGTTCAAAGgtatcattta ... attatggcagGTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTG
EST: gi|218482307|gb|FG954939.1|FG954939
EST:     AGCCAATGATGGAGGTCTTCTTGCTGCAATTATGGCTGCTGGGTTCAAAG                         GTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTG
genomic: AGCCAATGATGGAGGTCTTCTTGCTGCAATTATGGCTGCTGGGTTCAAAGgtatcattta ... attatggcagGTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatactgtgatttggaatagtctgtaatatttatgtgaataattcattatggcagGTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTGATGCTTGGTATTCTGATGGTCATGGTTCAGTAGAAAGCACTGCTGCATA
                      tgtaatatttatgtga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcatttatcgacactttatgatactgtgatttggaatagtctgtaatatttatgtgaataattcattatggcagGTGAACTCAATCGATTTCAACCTGGAGTTTCAATTGAAATATCACGGCTTGATGCTTGGTATTCTGATGGTCATGGTTCAGTAGAAAGCACTGCTGCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC