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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctcaacttctcatcacctattgacagccaaaataaaaaaaaaatctagtatttattatactttgtattacagtgttgtgtgacctgttttttttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTTCCGCTTT

Basic information

species Oryza sativa
transcript LOC_Os02g15550.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G060896_T04 (Zea mays), 3'ss of exon 4
gttctcaacttctcatcacctattgacagccaaaataaaaaaaaaatctagtatttattatactttgtattacagtgttgtgtgacctgttttttttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTTCCGCTTT
         ||| ||||| || || | | |  |||||| ||||||| || | ||||    || | ||| ||  |  || ||           | ||| ||||||||| || |||||||| ||||| ||||| |||||||||||||| ||||||||||| |||||||||||||| ||||||||||||||||||||||| || ||||
--------gttcacatcatctgttcataccagaaataagaaaaaaaact-gcatttggcttattctgt-ttgtaacgtggtaa---------tctttgtatgcagTCGTCGACCTATGGTAAAGTCCTTGTGCTTGATGGTATTGTTCAGTTGACTGACAAGGATGAATGTGCATACCAGGAAATGATTACTCACCTGCCACTTT

upper sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 3
gttctcaacttctcatcacctattgacagccaaaataaaaaaaaaatctagtatttattatactttgtattacagtgttgtgtgacctgttttttttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTTCCGCTTT
         ||||  |||  || ||| | |  ||||| |||     | | |    | || |     |||| ||            | ||| |||||| | ||||||| ||||||||||| ||||| ||||| |||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| || || |
--------gttcttttcatttactgatatcagaaatataaatttcctttggctcctgttgt-----gtataac------------cttgtattttttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCT

upper sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G13210.3 (Glycine max), 3'ss of exon 4
gttctcaacttctcatcacctattgacagccaaaataaaaaaaaaatctagt-atttattata--ctttgtattacagtgttgtgtgacctgttttttttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTTCCGCTTT
                                   |         ||||  | ||||| ||||   |||  || | |||| |   || |   |  |||| || ||||||| ||||  ||||| || || ||||| |||||||| || || || |||||||| | |||||||||||| |||||||| |||||  |||| ||||| || |
--------------------------------gtttggtctcttcatcttatgatttactataaattttacatgaaagtgataaatg-ctaatccttttgttttgcagTCATCAATGTATGGGAATGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAGGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT

upper sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 4
gttctcaacttctcatcacctattgacagccaaaataaaaaaaaaatctagtatt-tattatacttt--gtattacagtgttgtgtgacctgttttttttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTTCCGCTTT
                                   |         ||||  || | || ||||  ||     | | || | |   || |   |  |||  || ||||||| ||||| ||||| ||||| ||||| |||||||| || || || |||||||| |||||||||||||| |||||||| |||||  |||| ||||| || |
--------------------------------gtttggcctcttcatcttataatgtactataactttaacgtgaaagggatagatg-ctaatcctttcattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAAGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT

upper sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 4
-------gttctcaacttctcatcacctattgacagccaaaataaaaaaaaaatctagtatttat-tatactttgtattacagtgttgtgtgacctgt-------------------tttttttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTTCCGCTTT
        |||| ||||    ||   ||| ||     | || |  |   |   || | | ||||| |||   |  | ||    | || | |   || |                   || |||| | ||||||| ||| | ||||| ||||| ||||| |||||||| ||||| |||||||  || || ||||||||||| || ||||| |||||| |||||||||| ||||
gttctgcattctgaactctaaat--actagtgttgttcgaagttgacttagtttccattttttatctatctgtcatgttcttcttttctttcttctatattagctagctaatgcagattcttttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT

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|218497061|gb|FG955846.1|FG955846
EST:     AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAG                         TCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
genomic: AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAGgttctcaact ... ttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
EST: gi|58602035|gb|CK012563.1|CK012563
EST:     AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAG                         TCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
genomic: AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAGgttctcaact ... ttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
EST: gi|58695758|gb|CK084445.1|CK084445
EST:     AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAG                         TCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
genomic: AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAGgttctcaact ... ttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
EST: gi|29642051|gb|CB647058.1|CB647058
EST:     AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAG                         TCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
genomic: AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAGgttctcaact ... ttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
EST: gi|29672898|gb|CB669173.1|CB669173
EST:     AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAG                         TCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
genomic: AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAGgttctcaact ... ttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
EST: gi|11025755|gb|AU162356.1|AU162356
EST:     AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAG                         TCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
genomic: AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAGgttctcaact ... ttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
EST: gi|33793719|gb|CF322742.1|CF322742
EST:     AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAG                         TCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
genomic: AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAGgttctcaact ... ttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
EST: gi|29664250|gb|CB660525.1|CB660525
EST:     AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAG                         TCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
genomic: AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAGgttctcaact ... ttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
EST: gi|58678117|gb|CK066804.1|CK066804
EST:     GAAGTTTTAGTTTTTGAG                         TCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
genomic: GAAGTTTTAGTTTTTGAGgttctcaact ... ttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
EST: gi|33794317|gb|CF323046.1|CF323046
EST:     AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAG                         TCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
genomic: AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAGgttctcaact ... ttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACT
EST: gi|29667240|gb|CB663515.1|CB663515
EST:     AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAG                         TCCTCAACCTATGGAACAGTTCTTGTCCTTGATGGTATTGTCCCAGTTGAC
genomic: AGATCTTGTATCAGGGGAAGTCACCATACCAAGAAGTTTTAGTTTTTGAGgttctcaact ... ttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCC-AGTTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatttattatactttgtattacagtgttgtgtgacctgttttttttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTTCCGCTTT
                                   cctgttttttttttat  CT-rich tract
     tattatactttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctcaacttctcatcacctattgacagccaaaataaaaaaaaaatctagtatttattatactttgtattacagtgttgtgtgacctgttttttttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTTCCGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG