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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGGGGATCCTTTGGAGAATGGTACGTTACTGGGGCCATTGCACACTCCTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattattgatgcaacaacatttgcttgtgcatcaatgtctgtttgcattatattaaacaatctttacatcttcaatacttaaaatgcttaagttgg...

Basic information

species Oryza sativa
transcript LOC_Os09g26880.4
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g26880.4 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G130440_T02 (Zea mays), 5'ss of exon 10
AATTGGGGATCCTTTGGAGAATGGTACGTTACTGGGGCCATTGCACACTCCTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtga----tattattgatgcaacaacatttgcttgtgcatcaatgtctgtttgcattata---ttaaacaatctttacatcttcaatacttaaaatgcttaagttgg
|||||||||||| |||||||| || || |||||||| ||| |||||||||||||||||| ||| ||| ||||||||||| || || |||| ||||||||||| || | | || ||| || | | | || || | | ||||| | | | || | | | || | | | | | |
AATTGGGGATCCGTTGGAGAAAGGCACCTTACTGGGACCACTGCACACTCCTGCTTCAAAAGAGAACTTTTTGAAAGGCATTCAGACTATCAAATCTCAGgtgaaggttaaaagtagtgttacattatcggttcctacaattatttgaacctccattacaatctcactggatataaatagctatgagaatcatgttattc-------

upper sequence: LOC_Os09g26880.4 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G820733_T01 (Zea mays), 5'ss of exon 2
AATTGGGGATCCTTTGGAGAATGGTACGTTACTGGGGCCATTGCACACTCCTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtga----tattattgatgcaacaacatttgcttgtgcatcaatgtctgtttgcattata---ttaaacaatctttacatcttcaatacttaaaatgcttaagttgg
|||||||||||| |||||||| || || |||||||| ||| |||||||||||||||||| ||| ||| || |||||||| || || |||| |||| |||||| || | | || ||| || | | | || || | | ||||| | | | || | | | || | | | | | |
AATTGGGGATCCGTTGGAGAAAGGCACCTTACTGGGACCACTGCACACTCCTGCTTCAAAAGAGAACTTTTTAAAAGGCATTCAGACTATCAAATCTTAGgtgaaggttaaaagtagtgttacattatcggttcctacaattatttgaacctccattacaatctcactggatataaatagctatgagaatcatgttattc-------

upper sequence: LOC_Os09g26880.4 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G820733_T02 (Zea mays), 5'ss of exon 2
AATTGGGGATCCTTTGGAGAATGGTACGTTACTGGGGCCATTGCACACTCCTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCA-TCAGATCTCAGgtgatattattgatgcaacaacatttgcttgtgcatcaatgtctgtttgcattatattaaacaatctttacatcttcaatacttaaaatgcttaagttgg
|| | | | | | | |||| | ||| ||| ||| || ||||| | || || | || ||| ||| | || || | || | | || || | | | | | || ||| | || |
---------------------------ATTCTTCATGAGAATATATATCAAACCTTCCTTGATCAGCTTGTTG--AGgtatacaaacaagtccgaatt--ggggat-ccgttggagaaa-ggcaccttactg-ggaccactgcacactcctgcttcaaaagagaactttttaaaaggcattc-------------------

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|33364555|gb|BP432941.1|BP432941
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29669203|gb|CB665478.1|CB665478
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAGAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29655856|gb|CB652131.1|CB652131
EST:     GAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: GAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29674835|gb|CB671110.1|CB671110
EST:     GAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: GAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29638872|gb|CB643881.1|CB643881
EST:     CCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29665769|gb|CB662044.1|CB662044
EST:     GAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: GAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29668604|gb|CB664879.1|CB664879
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29619465|gb|CB624477.1|CB624477
EST:     CTGCTTCAAAAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAN                         NNNNNNAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29617472|gb|CB622484.1|CB622484
EST:     GAAAGGCATCCAAACCATCAGATCTCAN                         NNNNNNAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: GAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29670275|gb|CB666550.1|CB666550
EST:     CATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|58695697|gb|CK084384.1|CK084384
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAN                         NNNNNNAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29663938|gb|CB660213.1|CB660213
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|88571108|gb|CI662481.1|CI662481
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29629464|gb|CB634473.1|CB634473
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAN                         NNNNNNAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29656048|gb|CB652323.1|CB652323
EST:     AAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: AAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29639263|gb|CB644272.1|CB644272
EST:     AAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: AAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29673830|gb|CB670105.1|CB670105
EST:     TCAAGAGACGCCTTC-TGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: TCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29613124|gb|CB618137.1|CB618137
EST:     CTGCTTCAAAAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAN                         NNNNNNAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29663977|gb|CB660252.1|CB660252
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29628533|gb|CB633544.1|CB633544
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAN                         NNNNNNAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|66920685|gb|CX107533.1|CX107533
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29677489|gb|CB673764.1|CB673764
EST:     NTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29668647|gb|CB664922.1|CB664922
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAN                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29656046|gb|CB652321.1|CB652321
EST:     GAAAGGCATCCAAACCATCAGATTTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: GAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29668563|gb|CB664838.1|CB664838
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAT                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGANGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29668605|gb|CB664880.1|CB664880
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29667911|gb|CB664186.1|CB664186
EST:     CTGCTTCAAGAGACGCTTTCTTGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29623916|gb|CB628927.1|CB628927
EST:     AAAGGCATCCAAACCATCAGATCTCAN                         NNNNNNAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: AAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29667685|gb|CB663960.1|CB663960
EST:     CTGCTTCAAGAGACGCTTTCTTGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29633228|gb|CB638237.1|CB638237
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAN                         NNNNNNAAAAATTCTTTATGGANGGATCTGCAATTGAATCT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGG-AAAAATTCTTTATGGA-GGATCTGCAATTGAATCT
EST: gi|29628522|gb|CB633533.1|CB633533
EST:     AGGCATCCAAACCATCAGATCTCAN                         NNNNNNAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: AGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29664485|gb|CB660760.1|CB660760
EST:     TCAAAAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: TCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|88307624|gb|CI644660.1|CI644660
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29673253|gb|CB669528.1|CB669528
EST:     CAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29672296|gb|CB668571.1|CB668571
EST:     GAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: GAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|29668614|gb|CB664889.1|CB664889
EST:     AAGGCATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: AAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
EST: gi|58604471|gb|CK014999.1|CK014999
EST:     CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAN                         NNNNNNAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAG
genomic: CTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAG
EST: gi|29663939|gb|CB660214.1|CB660214
EST:     CATCCAAACCATCAGATCTCAG                         GGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT
genomic: CATCCAAACCATCAGATCTCAGgtgatattat ... taatttgcagGGGGGAAAAATTCTTTATGGAGGATCTGCAATTGAATCTGAGGGAAACTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGGGGATCCTTTGGAGAATGGTACGTTACTGGGGCCATTGCACACTCCTGCTTCAAGAGACGCCTTCTTGAAAGGCATCCAAACCATCAGATCTCAGgtgatattattgatgcaacaacatttgcttgtgcatcaatgtctgtttgcattatattaaacaatctttacatcttcaatacttaaaatgcttaagttgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA