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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT

Basic information

species Oryza sativa
transcript LOC_Os09g07510.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
-ggagcaaatagtgcatgat-tgagccagttgggac-atttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
  |    |||  | || |   | ||  | |||  |  | ||   |  ||  |  | ||   || || |   |   |  ||   |  || |  ||||    |||| |||||||| || ||  | ||||||||||| || ||||||||||||||||| |||||||| || |||||||||| ||||||||| || |||||||||||
ttgtttgaatgttacaaggcatcagttatttgaaattagttcacagtcaaatcataca--ttacatcagctaagaagaaactgttttgactctttaac-tcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 3
-ggagcaaatagtgcatgat-tgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
  |  ||  |  |   |  | | |      || |   ||||   |  || | ||| |   |  |||    | || |  || ||  |  |||| |  |  ||||||||||||| || ||  |  | || ||||| || ||||| ||||| ||||||||||||||||| |||||||| || |||||||| ||||| || || ||
atgttcatttgttaagtagtgttattttactgtgttttttaa-gttgatctgctggaag-tgcatacattaactgatgatttttttatccttgttcttgcagATCAAGATTCTGTTCGGCTACTTGCTGTTGAGGGTTGTGCAGCTCTGGGGAAATTGTTGGAACCTCAAGATTGCGTGGCACATATTCTTCCTGTCATAGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 3
----------------------ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
                              |  ||  |      | || |    |  |  |  ||| || |||   |    || |     |     |||| |  ||             |||||||||| || ||  | |||||||| || || || |||||||||||||||||| || |||| |||||||||||  |  ||||||| || ||         
gtaattgaatacatatttctcattctttcttgatgtcttggcctgtcaatcataaattcaataataaattttccttaatacaattggcctagtatgcaatttaactttttaacctggctcagATCAAGACTCTGTTAGATTGTTGGCTGTGGAGGGTTGTGCTGCTCTTGGGAAACTGCTGGAGCCACAAGATTGCATCACACATATACTACCG--------

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 3
----------------------ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
                              |  ||  |      | || |    |  |  |  ||| || |||   |    || |     |     |||| |  ||             |||||||||| || ||  | |||||||| || || || |||||||||||||||||| || |||| |||||||||||  |  ||||||| || || ||||||||
gtaattgaatacatatttctcattctttcttgatgtcttggcctgtcaatcataaattcaataataaattttccttaatacaattggcctagtatgcaatttaactttttaacctggctcagATCAAGACTCTGTTAGATTGTTGGCTGTGGAGGGTTGTGCTGCTCTTGGGAAACTGCTGGAGCCACAAGATTGCATCACACATATACTACCGGTTATTGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 3
-------------------------------ggagcaaatagtgcatgattgagccagttgggacatttac-----tatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattacc-------agATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
                               |  | |||  ||   | |||  | | |||   | ||||||     |     |||| |  || ||    |||| |  | ||    ||  |   |  || | | |       |||||||||||| ||  | |||||||| || || ||||||||||||||||| ||  ||||||| |||||||||||||| |||||||| || || ||||||||
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcattt-gtctgttac-atatttacatgtgtgattgtgttgtagagtctcctgaatgtactttactcctttaatatgcaattgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 2
-ggagcaaatagtgcatgat-tgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
  |  ||  |  ||  |  | | |      || |   ||||   |  ||   ||| |   |  |||    | || |   | ||  |  |||| |      |||||||||||| || ||  |  | || ||||| || ||||| ||||| || |||||||||||||| ||||||||||| |||||||| ||||| || || ||
atgttcatttgttgagtagtgttattttactgtgttttttaa-gttgatccgctggaag-tgcatacattaactgatggtttttttatccttgttcctgtagATCAAGATTCTGTTCGGCTACTTGCTGTTGAGGGTTGTGCAGCTCTGGGAAAATTGTTGGAACCTCAAGATTGTGTGGCACATATTCTTCCTGTCATAGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 3
-------------------------------ggagcaaatagtgcatgattga-gccagttggg-----acatttactataca--tgttctgcag-----cctaaataa---tgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
                               |  | |||  ||   | |||   | |  |||       |||||   | |     |||  || ||     ||| |||     | | |||   |||||   | |   | |   | ||||||||||||| ||  | |||||||| || || ||||||||||||||||| ||  ||||||| |||||||||||||| |||||||| || || ||||||||
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttttgtctattgcatatttacattggttgtgtgattgtgttgtagaatctcctgaatgtactttcctcttttaatatgtgttgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------------------------------------------------------ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
                                                                                                  |  |||   ||  ||||  |     ||||    ||  || | ||         |  | |    ||| | ||    |    ||      ||  |  |||| |||||||| ||  |  | ||||| |||||||| ||||| |||||||| || ||||||||||| || |||||||| ||||  ||  | || ||||||||
gtacttaatgtttgaatatatcgtactttatatgtgctcatcacttagaaatagtttgcatagacccaagagtatggtaaagagatcacatttgaattaataaacgctgtttgatgaaatatattggatacttacctcttcagaaatgtttgttttatctgtgcttatattggttaaactttaaccttcatttcagACCAAGATTCTGTGAGACTATTGGCTGTTGAAGGGTGTGCAGCTCTTGGAAAGTTGTTGGAACCTCAGGATTGTGTTGCACGCATTTTACCTGTTATTGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 2
ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttat-taccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
                 ||||| |    || | | |||| |     |  ||| |||| || ||| |   || ||    ||     |  ||||   || ||||||||||||| ||  | || ||||| ||||| || |||||||||||||||||||||||||| || || ||||||||   ||| || ||||| || |||||
---------------gtattgaac--actgag-cgtttatt-----tactctacagcatatata-tttgtcgaatttcatcttacgtttttttcatatcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G13320.3 (Arabidopsis thaliana), 3'ss of exon 3
ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagccta-aataatgca---tctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
     || |   |||  |||  |   ||    |  |   ||  |     | |  |   || |||| | ||   | |||  || ||  || | ||    || ||||||||||||| ||  | || ||||| ||||| || |||||||||||||||||||||||||| || || || ||||| ||||| || ||||| || |||||
--ctgaagttaagcagaattacggttgtctacatctcagcttcagtgtctttttatattataatattacagattttaagtatcttattgacatt--gatatcagATCAAGATTCGGTTAGATTATTGGCTGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCCCAGGACTGTGTTGCACACATTCTTCCTGTGATTGT

upper sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 4
ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggcct----tttattacca-----gATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
      |||    ||   |||      ||  |   ||  |  ||  | || |  |    || ||    | | |      ||| | || |    ||||||  ||     ||||||||||| ||  | || ||||| ||||| || ||||| ||||| || ||  |||||||||| |||||||||||||||||||| ||||| || |||||
------aatg--acaaagttgtttttctttcgtttttgccggtat-ttttttatattggaagtatgatagccatttgggttgttagcttacaatttattttcatttcagATCAAGATTCTGTTAGGTTATTGGCTGTTGAGGGTTGTGCAGCTCTCGGAAAGCTGTTGGAACCTCAAGATTGTGTAGCACATATTCTTCCCGTAATTGT

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|300215963|gb|HO088589.1|HO088589
EST:     CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATG                         ATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
genomic: CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATGgtaccatgca ... ttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
EST: gi|58672176|gb|CK060862.1|CK060862
EST:     CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATG                         ATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
genomic: CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATGgtaccatgca ... ttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
EST: gi|300215769|gb|HO088395.1|HO088395
EST:     CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATG                         ATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
genomic: CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATGgtaccatgca ... ttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
EST: gi|29658915|gb|CB655190.1|CB655190
EST:     CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATG                         ATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
genomic: CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATGgtaccatgca ... ttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGA
EST: gi|313081057|gb|HO213643.1|HO213643
EST:     CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATG                         ATCAAGATTCCGT
genomic: CTATCTAAAGACAGAAGTCATGTCGATATTTGATGATCTAACCCAAGATGgtaccatgca ... ttattaccagATCAAGATTCCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
                       atctaac  putative branch site (score: 2)
                                         ccttttatt  putative PPT
                          taacaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttattaccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT

-gagcaaa
- - - - - -tgcatga
- - - - - - - - - - - - - - - - - - - - -atacatg
- - - - - - - - - - - - - - - - - - - - - - - - - -tgcagcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctggc