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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaccttctgtttttaggctgcatgcttgattctattcaacataacttggcctgtttttcttaatatcatgttatattgcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCTAGGTTGGACGCACAGCAGAAGAAGCTCAACCTTCCAGTCCTTCCTACAA

Basic information

species Oryza sativa
transcript LOC_Os12g42884.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42884.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G149751_T06 (Zea mays), 3'ss of exon 6
gtaagtaccttctgtttttaggctgcatgcttgattctattcaacataacttggcctgtttttcttaatatcatgttatattgcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCTAGGTTGGACGCACAGCAGAAGAAGCTCAACCTTCCAGTCCTTCCTACAA
|||||||||||      | |||||  |    | |  |     |    |  || |    | | |   |   || |  || ||  ||  | |||||||||||||| | ||| ||||||||||||||||  ||||| ||||| ||||| ||||| || |||||||||||||| ||||| ||  ||||||| || |
gtaagtaccttg---cctgaggcttaaaagctaacacatgctagtccagttttg---atgtgtaccagcctctttctacat-actgttacagGCTGCTGCTCTCAAGGGCTCTGACCACCGCCGTGGGACCAACGTTAGTGCTAGATTGGATGCCCAGCAGAAGAAGCTTAACCTCCCCATCCTTCCCACCA
















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|300215517|gb|HO088143.1|HO088143
EST:     CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCT                         GCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCTCT
genomic: CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtacct ... gcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
EST: gi|218492493|gb|FG951515.1|FG951515
EST:     CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCT                         GCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
genomic: CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtacct ... gcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
EST: gi|300216253|gb|HO088038.1|HO088038
EST:     CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCT                         GCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCTCT
genomic: CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtacct ... gcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
EST: gi|11863315|gb|AU065792.2|AU065792
EST:     CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCT                         GCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
genomic: CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtacct ... gcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
EST: gi|29637650|gb|CB642659.1|CB642659
EST:     CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCT                         GCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
genomic: CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtacct ... gcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
EST: gi|29675799|gb|CB672074.1|CB672074
EST:     CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCT                         GCTGCTGCTCTGAGGGGGTCTGACCACCGACGTGCTACC
genomic: CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtacct ... gcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACC
EST: gi|58613186|gb|CK040898.1|CK040898
EST:     CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCT                         GCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
genomic: CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtacct ... gcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
EST: gi|218483058|gb|FG951439.1|FG951439
EST:     CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCT                         GCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
genomic: CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtacct ... gcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
EST: gi|4968885|gb|AU065789.1|AU065789
EST:     CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCT                         GCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
genomic: CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtacct ... gcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
EST: gi|428283|gb|D24431.1|D24431
EST:     CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCT                         GCTGCTGCTCTNAGGGGG
genomic: CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtacct ... gcttgtgcagGCTGCTGCTCTGAGGGGG
EST: gi|29615679|gb|CB620691.1|CB620691
EST:     CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCT                         GCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCTCT
genomic: CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtacct ... gcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
EST: gi|29635138|gb|CB640147.1|CB640147
EST:     CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCT                         GCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTA
genomic: CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtacct ... gcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTA
EST: gi|33800724|gb|CF326232.1|CF326232
EST:     CCTCCAGGAGGTCATCACCTCGTGTTACAAACGAGGAAGTCCAAAAGGCT                         GCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
genomic: CCTCCAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtacct ... gcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT
EST: gi|58661898|gb|CK050578.1|CK050578
EST:     CAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCT                         GCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCTCT
genomic: CAGGAGGTCATCACCTCGTGTGACAAACGAGGAAGTCCAAAAGGCTgtaagtacct ... gcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcaacataacttggcctgtttttcttaatatcatgttatattgcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCTAGGTTGGACGCACAGCAGAAGAAGCTCAACCTTCCAGTCCTTCCTACAA
                         tcttaat  putative branch site (score: 3)
                     tttttcttaatatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaccttctgtttttaggctgcatgcttgattctattcaacataacttggcctgtttttcttaatatcatgttatattgcttgtgcagGCTGCTGCTCTGAGGGGGTCTGACCACCGCCGTGCTACCAATGTTAGCGCTAGGTTGGACGCACAGCAGAAGAAGCTCAACCTTCCAGTCCTTCCTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA