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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaatctatttgttatcttcctatacttaggaagtaacctgtctcatcaacttctttttttccttttgcttttttgacag

Basic information

species Oryza sativa
transcript LOC_Os06g10280.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g10280.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G701058_T02 (Zea mays), 5'ss of exon 4
TGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaatcta----tttgttatcttccta-tacttaggaagtaacctgtc---tcatcaacttctttttttc--cttttgcttttttg-acag
|||| || |||||||| || || || || ||||||||||||||||||||||| |||||||||||||||||||||| || |||         |   | |  || || | || || ||  | |||  |   |  | ||| ||| ||   |  ||  || | ||    ||||
TGGGTCTCTACCTGCACCTCGCTGTGTCGGTTGTGCATGAAATCAAGGATGCCCTTGGAATCTATTGCTTCAGgtgtggaaactggaaacctccgtgtgctcttactgctcagaaaccaccctcccatgtttttaacctctcttccgctgctgctggtattgcatacag
















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|88536305|gb|CI466049.1|CI466049
EST:     GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG                         GATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
genomic: GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaat ... tttttgacagGATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
EST: gi|88559034|gb|CI489572.1|CI489572
EST:     AAATCAAGGATGCTCTTGGAATCTATTGCTTCAG                         GATAACTAGAAAAGAGGCTTGAATGTNTTCTGAGTTCTTACATAGCAATAG
genomic: AAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaat ... tttttgacagGATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
EST: gi|88469175|gb|CI406446.1|CI406446
EST:     GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG                         GATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
genomic: GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaat ... tttttgacagGATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
EST: gi|88265983|gb|CI376885.1|CI376885
EST:     GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG                         GATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
genomic: GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaat ... tttttgacagGATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
EST: gi|86861509|gb|CI328196.1|CI328196
EST:     GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG                         GATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
genomic: GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaat ... tttttgacagGATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
EST: gi|86435856|gb|CI107089.1|CI107089
EST:     GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG                         GATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
genomic: GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaat ... tttttgacagGATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
EST: gi|86425382|gb|CI070479.1|CI070479
EST:     GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG                         GATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
genomic: GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaat ... tttttgacagGATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
EST: gi|86536568|gb|CI176774.1|CI176774
EST:     GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG                         GATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
genomic: GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaat ... tttttgacagGATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
EST: gi|86869993|gb|CI317914.1|CI317914
EST:     GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTA-TGCTTCAG                         GATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
genomic: GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaat ... tttttgacagGATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
EST: gi|88551458|gb|CI481515.1|CI481515
EST:     GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG                         GATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
genomic: GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaat ... tttttgacagGATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
EST: gi|88254291|gb|CI352917.1|CI352917
EST:     AATCTATTGCTTCAG                         GATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
genomic: AATCTATTGCTTCAGgtctgtaaat ... tttttgacagGATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
EST: gi|89163723|gb|CI100613.1|CI100613
EST:     GCTCTTGGAATCTATTGCTTCAG                         GATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
genomic: GCTCTTGGAATCTATTGCTTCAGgtctgtaaat ... tttttgacagGATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
EST: gi|88524956|gb|CI453573.1|CI453573
EST:     TNTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG                         GATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
genomic: T-TTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaat ... tttttgacagGATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
EST: gi|38483180|gb|CF966982.1|CF966982
EST:     GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG                         GATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
genomic: GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaat ... tttttgacagGATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
EST: gi|88250958|gb|CI349188.1|CI349188
EST:     GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAG                         GATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG
genomic: GTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaat ... tttttgacagGATAACTAGAAAAGAGGCTTGAATGTGTTCTGAGTTCTTACATAGCAATAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGCCTTTACCTGCATCTTGCCGTTTCTGTTGTGCATGAAATCAAGGATGCTCTTGGAATCTATTGCTTCAGgtctgtaaatctatttgttatcttcctatacttaggaagtaacctgtctcatcaacttctttttttccttttgcttttttgacag

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