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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgatgatctttggaaacaactctcttattcaatttgattctcataaaccctaaatcttaaacccttttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATGGAGGGAACGAAGGGACGAAGCAAGGTGCTCAGAGAAGTACAAGGAGATC

Basic information

species Oryza sativa
transcript LOC_Os01g25189.4
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g25189.4 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G473533_T07 (Zea mays), 3'ss of exon 2
gtga-tgatgatctttggaaacaactctcttattcaattt-gattctcataaaccctaaatcttaaacccttttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATGGAGGGAACGAAGGGACGAAGCAAGGTGCTCAGAGAAGTACAAGGAGATC
|||| |||  || ||  |   ||  || |||   || |   |   |  || |||    |||||| | ||   ||  |||||||| ||| |||||||||||||||| || |||||| ||||| | ||| | | ||||||| |  | || || || ||||||||  ||||||||| |||||||
gtgagtgaccattttctgtggcagttccctttcgcagtggaggcacgtatgaac----aatcttgatccaacttt-tgcagTTCCGTGGTCCCATACTTCTACCCCACGTACCTGCTCATTCTACTGGTCTTGAGGGAAAGGCGCGATGAGGCGAGGTGCTCGCAGAAGTACAGGGAGATC
















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|88522833|gb|CI450626.1|CI450626
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88532936|gb|CI462268.1|CI462268
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88551911|gb|CI482008.1|CI482008
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88376078|gb|CI530582.1|CI530582
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88527617|gb|CI455791.1|CI455791
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGTGCAG                     
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAA-C----CAGgtgatgatga ... tttagt
EST: gi|88555636|gb|CI485908.1|CI485908
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88478942|gb|CI416213.1|CI416213
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88533815|gb|CI460483.1|CI460483
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|33689268|gb|CF317507.1|CF317507
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGTGCAG                     
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAA-C----CAGgtgatgatga ... tttagt
EST: gi|88542985|gb|CI472349.1|CI472349
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88554518|gb|CI484704.1|CI484704
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGTGCAG                     
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAA-C----CAGgtgatgatga ... tttagt
EST: gi|88532876|gb|CI461323.1|CI461323
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88537897|gb|CI466882.1|CI466882
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88552415|gb|CI482419.1|CI482419
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88549113|gb|CI478971.1|CI478971
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88840388|gb|CI079842.1|CI079842
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TGCAGTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagT----T-CGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTG
EST: gi|88554216|gb|CI484383.1|CI484383
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88550467|gb|CI478444.1|CI478444
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88546361|gb|CI475991.1|CI475991
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|87015902|gb|CI279654.1|CI279654
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88536421|gb|CI466172.1|CI466172
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTAATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88227443|gb|CI226923.1|CI226923
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88553441|gb|CI483555.1|CI483555
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
EST: gi|88527939|gb|CI456136.1|CI456136
EST:     CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG                         TTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG
genomic: CTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAGgtgatgatga ... tttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcttattcaatttgattctcataaaccctaaatcttaaacccttttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATGGAGGGAACGAAGGGACGAAGCAAGGTGCTCAGAGAAGTACAAGGAGATC
                           ccctaaa  putative branch site (score: 3)
                                         ccctttt  putative PPT
     tattcaatttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgatgatctttggaaacaactctcttattcaatttgattctcataaaccctaaatcttaaacccttttagtgcagTTCGGTGATCCCATACTTCTACCCAACATACCTGTTCATTTTGCTGATATGGAGGGAACGAAGGGACGAAGCAAGGTGCTCAGAGAAGTACAAGGAGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC