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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtactagaaacaatttgaaatatggatcctttccaacatccaattctgctgcaatcatgctggtttctttttacaactttcctattcctgtttggtagATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG

Basic information

species Oryza sativa
transcript LOC_Os06g03760.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 4
-----ctgtactagaaacaatttgaaatatggatcctttccaacatccaattctgctgcaatcatgctggtttctttttacaacttt-cctattcctgtttggtagATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG
     |||   |  |       || ||  ||    | | |   |||| ||||||   ||| |  | ||  ||  || |   |||| | |||  | || |||||||||||||||||||||| |||||||| |||||||||||||||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||||||||||
ttcgcctgccatttagtactcctgtaacttgtcatcatgctgtcatc-aattct---gcattttttct--ttcattctgctaactataccttattctttttggtagATATTTGGTGGTGTCGGAATTGCCTGCCTTCCATTGGGACTTATATTCTCATTTGTTCGGCGTCCAAAAGCTGTAATTACACGCTCACAATATATAAAG

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 2
-ctgtactagaaacaatttgaaatatggatcctttccaacatccaattctgctgcaatcatgctggtttctttttacaactttcctattcctgtttggtagATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG
 ||   ||   |   | |     |||      |  |||   |  |||  | |||||||  |  |  ||  || |   |||| | |  || || |||||||||||||||||||||| |||||||| |||||||||||||||||||||||||||||||| || || ||||||||||| ||||||||||||||||||||||||
gctcacctgtcatttagtactgctataacctgtaaccatgctgtaatcgttctgcaatt-ttttctttcattctgctaactataccttttctttttggtagATATTTGGTGGTGTCGGAATTGCCTGCCTTCCATTGGGACTTATATTCTCATTTGTTCGTCGTCCAAAAGCTGTAATTACACGCTCACAATATATAAAG

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 4
ctgtactagaaacaatttgaaatatg-gatcctttccaacatccaattctgctgcaatcatgctggtttctttttacaactttcctattcctgtttggt--agATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG
   |  ||  |||  | | || | |   ||||      ||||  | || |  |    ||||  | ||   | |  || | | |  | || |  ||   |  ||||||||||||||||||| |||||||| |||||||||||||||||||| |||||  | || || ||||| ||||| || || || ||||| ||||| |||
tacttgtaataactttctaaagtcttcaatcccaggtcacatttacttttatttt--tcatattagtga-tatcaactattgttttctttccattcaatccagATATTTGGTGGTGTTGGTATTGCTTGTCTTCCATTGGGACTTATATTTTCATTCATTCGACGTCCAAAGGCTGTTATCACTCGTTCACAGTATATCAAG

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G30400.1 (Glycine max), 3'ss of exon 4
ctgtactagaaacaatttgaaatatggatcctttccaacatccaattctgctgcaat---catgctggtttctttttacaactttcctattcctgtttggt--agATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG
 |  |||  | | ||   |||  ||  ||   |||| |  ||  |||    |  | |   |||  | ||   | || |||| | |  | || |  ||   |  ||||||||||||||||||| |||||||| |||||||||||||||||||| |||||  | ||||| ||||| ||||| || || || ||||| ||||| |||
-taaactgtacaaaa---gaagaatcaattacttcccaggtcatatttacttttatttttcatattagtga-tattaacaattgttttctttccattcaatccagATATTTGGTGGTGTTGGTATTGCTTGTCTTCCATTGGGACTTATATTTTCATTCATTCGGCGTCCAAAGGCTGTTATCACTCGTTCACAGTATATCAAG

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 4
ctgtactagaaacaatt---tgaaatatggatcctttccaacatccaattctgctgcaatcatgctggtttctttttacaactttcctattcctgtttggt--agATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG
   || | ||   | ||   | |    |  || ||     ||||  | | || ||     ||| || | |   ||| || | | |  | |  |||||   |  ||||||||||||||||||| ||||| || |||||||| ||||||||||| |||||| | ||||| ||||| ||||| || || |||||||| ||||| |||
---taatggatttatttaaataagcctttcatactaaatcacattaagtacttcttttcccattcttgata--tttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCACAGTATATCAAG

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 4
ctgtactagaaacaatttgaaatatggatcctttccaacatccaattctgctgcaatcatgctggtttct---ttttacaactttcctattcctgtttggt--agATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG
   || | ||   |  || || || |  | |  | | | |||  |||  ||   | |  | ||  | |     ||| || | | |  | |  |||||   |  ||||||||||||||||||| ||||| || |||||||| ||||||||||| |||||| | ||||| ||||| ||||| || || ||||| || ||||| |||
---taatggattta--tttaagtaagccttccattctaaatcacattaagcgctagttgtcctattcttgatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATCACTCGCTCGCAGTATATCAAG

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 3
ctgtactagaaacaatttgaaatatggatcctttccaacatccaattctgctgcaatcatgctggtttct---ttttacaactttcctattcctgtttggt--agATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG
   || | ||   |  || || || |  | |  | | | |||  |||  ||   | |  | ||  | |     ||| || | | |  | |  |||||   |  ||||||||||||||||||| ||||| || |||||||| ||||||||||| |||||| | ||||| ||||| ||||| || || ||||| || ||||| |||
---taatggattta--tttaagtaagccttccattctaaatcacattaagcactagttgtcctattcttgatatttaaccattgttttctcactgttcaatccagATATTTGGTGGTGTTGGTATTGCCTGTCTTCCATTAGGACTTATATTTTCATTTATTCGGCGTCCAAAGGCTGTTATAACTCGCTCGCAGTATATCAAG

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------------------------------------------------ctgtactagaaacaatttgaaatatggatcctttccaacatccaattctgctgcaatcatgctggtttctttttacaactttcctattcctgtt-tggtagATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG
                                                                                     ||    |     |  ||  |  ||     | |||   |  |   ||| |  |||  || | ||      | |    |||| |  |||  |   | | ||||||||||||||||||||| ||||||||||| || ||||| |||||     ||||  || |||| ||||| ||||| || || || ||||| |||||||||
gtatgtacatctctctattaggtgttttgtgttaaaagtttcacctcattgtcttggaaggcatataatctttctcatattaaggcttggttgtgttctcttgcagttaaaagacttttggtagctgtgatttt-ttgctttcct-ctaaagattctgagaaactcttttatctcaaatgttgtagATATTTGGTGGTGTTGGTATTGCTTGCCTACCCTTGGGCCTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGGTCACAGTATATAAAG

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 4
ctgtactagaaacaatttgaaat--atggatcctttccaacatccaattc---tgctgcaatcatgctggtttctttttacaactttcctattcctgtttggtagATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG
     | ||| | ||||    ||  || ||         |  |   |||       | || | |      | |  |     || | | || |      ||  |||||||||||||||||||| ||||| || || ||||| ||||||||     ||||  || |||| ||||| ||||| || || || |||||||||||||||
----gcaagatataattctgtatccattgaagtaaatagatgtttgatttatacatttcagtaaaaaaaatctgataac-taattgttctctcaaatatttctagATATTTGGTGGTGTTGGTATTGCATGTCTACCATTAGGACTTATCACTGCATTCATCAGGCGACCAAAGGCTGTTATCACTCGATCACAATATATAAAG

upper sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 4
ctgtactagaaacaatttgaaatatggatcctttccaacatccaattctgctgcaatcatgctggtttctt-tttacaactttcctattcc-tgtttggt--agATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG
  |   ||| |  || ||| ||  |      |||   |  |  | || |  |    | ||    || | || || ||  |||| | |||   ||||   |  |||||||||| || ||||| ||||||||  | ||||||||||||||||| |||||  | ||||| || || ||||| || ||||| ||||| ||||| |||
--gagataggataaaattggaaagtta--tgttttagatctggattttttttctttttataaaagtattttattcacttcttttccatttgatgttctatccagATATTTGGAGGGGTTGGTATTGCTTGTTTGCCATTGGGACTTATATTTTCATTCATTCGGCGTCCCAAGGCTGTTATCACACGTTCACAGTATATCAAG

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|58680419|gb|CK069106.1|CK069106
EST:     CTGAATATGTGGTTGCTCTTGCTACCATCGTTGGATCTGTTCTCTTCACA                         ATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCA
genomic: CTGAATATGTGGTTGCTCTTGCTACCATCGTTGGATCTGTTCTCTTCACAgtgagtttta ... tgtttggtagATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCA
EST: gi|58671154|gb|CK059840.1|CK059840
EST:     CTGAATATGTGGTTGCTCTTGCTACCATCGTTGGATCTGTTCTCTTCACA                         ATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCA
genomic: CTGAATATGTGGTTGCTCTTGCTACCATCGTTGGATCTGTTCTCTTCACAgtgagtttta ... tgtttggtagATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCA
EST: gi|88730217|gb|CI753832.1|CI753832
EST:     CTGAATATGTGGTTGCTCTTGCTACCATCGTTGGATCTGTTCTCTTCACA                         ATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCA
genomic: CTGAATATGTGGTTGCTCTTGCTACCATCGTTGGATCTGTTCTCTTCACAgtgagtttta ... tgtttggtagATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCA
EST: gi|33381043|gb|CF196386.1|CF196386
EST:     CTGAATATGTGGTTGCTCTTGCTACCATCGTTGGATCTGTTCTCTTCACA                         ATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCA
genomic: CTGAATATGTGGTTGCTCTTGCTACCATCGTTGGATCTGTTCTCTTCACAgtgagtttta ... tgtttggtagATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgctgcaatcatgctggtttctttttacaactttcctattcctgtttggtagATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG
                                 ctttcctattcctgtt  CT-rich tract
                    tttcttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtactagaaacaatttgaaatatggatcctttccaacatccaattctgctgcaatcatgctggtttctttttacaactttcctattcctgtttggtagATATTTGGTGGTGTTGGAATTGCTTGCCTTCCATTGGGACTTATATTCTCATTTGTCCGGCGCCCAAAAGCTGTCATTACACGCTCACAATATATAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG