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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccctttgaaccatttggtgaaatgaaacatttgttttgtctcattgtaaaaaagtacatgcaaatataaatattcgttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG

Basic information

species Oryza sativa
transcript LOC_Os06g13820.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 14
------ccctttgaaccatttggtgaaatgaaacatttgttttgtctcattgtaaaaaagtacatgcaaatataaatattcgttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG
      |   || ||||| || |    |||      | ||   |   |||| | |   | |  |   || |  | ||||  |   ||| | |   ||  ||| ||||||||||||| |||||||| |||||||| ||||| ||||| |  || |||||||| || |||||||| || ||||||
gatgagctgcttcaaccactttgc---atgtgttcatggtagcgatacattttgattgatttga--gaagttaacatataagcatattct-tctgttcctctgcagGTTACCTTTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGCAAAAGATGGTTTGTTCTTAATGAGAAGAGTGGAAAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 2
---ccctttgaaccatttggtgaaatgaaacatttgttttgtctcattgtaaaaaagtacatgcaaatataaatat-tcgttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG
      ||| |||  | | |        |||  ||| || |    |           |      | |  ||||  | |  |||  ||  |   ||  | | |||||||||| || |||||||| |||||||| ||||| |||||||  ||||||||||| || |||||||| || ||||||
gttgtatttcaac--tctagcctgtcctaac--ttgcttgggactaaaaggctttgttgttgtgagaagtaaacctataattatattcttctgttcctatgcagGTTACCTCTTAAAGAAAAGCGCAAAAACTAATGGGTGGAGTAAAAGGTGGTTTGTTCTTAATGAGAAGAGTGGAAAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 14
ccctttgaaccatttggtgaaatgaaacatttgttttgtctcattgtaaaaaagtacatgc-----aaatataaatattc----gttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG
      || | ||  | | ||||  |  | ||     ||  || |||   |||||| ||       || ||| ||||  |      || |||| |  ||| || |||||| |   | || ||||||||||||||||| ||||| ||||| ||| | |||||||| || ||||| || |  ||||||
------gagctat--gcttaaatacatgaatttggaagttacaatgtgccaaagtatatatttcaaaattattaataaactaaaactacttttctttattgtt-ttcagGATTTTTATTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAAAAGACAGGAAAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 14
-ccctttgaaccatttggtgaaatgaaacatttgttttgtctcattgtaaaaaagtacatgcaaata-taaatattcgttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG
  |   ||    | |   |||| |   | | ||||  |||  ||  ||| | |  |  |    | || ||||       || |||| |  ||| || | |||| |   | || ||||||||||||||||| ||||| ||||| ||| | |||||||| || |||||||| |  ||||||
agctaatgcttaaatgcatgaatttgga-agttgtaatgtgccaaagtatatatttcaaaattattaataaactaaaactacttttctttattgtt-tgcagGATTTTTGTTAAAGAAAAGTGCAAAAACTAATGGTTGGAGCAGGCGATGGTTTGTGCTAAATGAGAAGACAGGAAAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 14
----ccctttgaaccatttggtgaaatgaaacattt--gttttgtctcattgtaaaaaagtacatgcaaatataaatattcgttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG
      |||||| | |    ||   || |    ||   |||||   |  || ||||||   || ||| ||  |    |   |  |||||| | |  | || | |||| ||| |  |||||||||||||||| |||||||| ||||||||| | |||||||| || ||||| ||||  ||||||
ctttagctttgacctagc--gtaggataagtttttgaggttttagtttgttataaaaaccaac-tgccaaggtcttcaacaga-aattttattc--tgttgtgcagGGTACTTAATGAAGAAAAGTGCAAAGACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAAAAAACTGGAAAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 14
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 14
---ccctttgaaccatttggtgaaatgaaacatttgttttgtctcattgtaaaaaagtacatgcaaatataaatattcgttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG
       ||    ||| |  |    |     ||   ||    || | |  | |||| ||  | | ||  || |||      |||  |     ||||  || ||| ||| |  ||||||||||||||||||||||||| ||||||||| | |||||||| || ||||||||||  ||||||
tgcatgatttcttcatgtctttttcttctttatcacttaaaactaacttgacaaaactaacttccaaggtagata---acaaatacttactcttttcatttagGGTACTTAATGAAGAAAAGTGCAAAAACAAATGGGTGGAGTAGGCGATGGTTTGTTCTGAATGAGAAAACTGGAAAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 14
-----------ccctttgaaccatttggtgaaatgaaacatttgttttgtctcattgtaaaaaagtacatgcaaatataaatattcgttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG
              | || | | | |  || |   | |  | |  | | ||||  | |       |   |     | |    |  | || | ||| ||||| |     |||| |  || ||||||||||||| |||||| ||||||||||| ||| | ||||||||  | ||||| || |  || |||
ataatggcatgtattgtgcatcttctcttgtatcaacatctct-ctctctctctctctc------tctctctctctctctccaaccttttactttatacatata----cagGCTTTCTATTGAAGAAAAGTGAAAAAACTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAG

upper sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 14
----------------------------------------------------------------------------------------------ccctttgaaccatttggtgaaatgaaacatttgttttgtctcattgtaaaaaagtacatgcaaatataaatattcgttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG
                                                                                                || |  | |||   ||  | ||    |   |  |||  | ||||   | |  ||  |       ||| |  || |  ||||| ||  ||| ||| |||| |   | ||||||| ||| || ||||||||||||||||||||| | ||||||||  | |||||||||||  | |||
gtgcttgagcgaacaatcagcattttaacttttgtggttctaaaaaatatggaattgtactatctacctgcagtcaacagttgttggacatgccttctctacatcatc-agtagagtgttggagaaggcttgcataattg-gtatatttatttattttattaacttgtcatcgattttttatttttatctgcagGATTTTTATTGAAGAGAAGCGCCAAAACAAATGGATGGAGTAGGCGATGGTTTGTTTTAAATGAGAAAAGTAGTAAG

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|33795777|gb|CF323758.1|CF323758
EST:     AGAGGGGTCCTCTGTGCAGGTTGCTGGTTCTTCTGGTGAAATTACTGCAG                         GTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGT
genomic: AGAGGGGTCCTCTGTGCAGGTTGCTGGTTCTTCTGGTGAAATTACTGCAGgtaagaatgt ... ttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaaaaagtacatgcaaatataaatattcgttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG
                             cgttaat  putative branch site (score: 4)
                                          catttttcttc  putative PPT
                aaatataaatattcgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccctttgaaccatttggtgaaatgaaacatttgttttgtctcattgtaaaaaagtacatgcaaatataaatattcgttaattttgtacatttttcttcagGTTACCTTTTGAAGAAAAGTGCAAAAACAAATGGATGGAGTAGGAGGTGGTTTGTCCTCAATGAGAAAAGCGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA