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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattaccagttcatatagaaaatatttgctgaccttcttgtggttattttaatcaaagtttagttgtataaattacattttatttaccttgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTG

Basic information

species Oryza sativa
transcript LOC_Os12g03060.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03060.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G318871_T01 (Zea mays), 3'ss of exon 1
aaattaccagttcatatagaaaatatttgctg-accttcttgtggttattttaatcaaagttta-------gttgt------ataaattacattttatttaccttgctcg-ccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTG
               ||   ||||||||  || |||||    ||||||||| |   | | | ||         |||      || |  ||||||  ||  |||||| ||  ||||||||   ||||||||  |||| ||  | ||| | || || ||| | || |||||||||||||  ||||||||||| ||||||||||| ||||||||||| 
---------------atgacaaatatttattgtacctttaaatggttatttaagcaagaatatatgagcttactgtcctagaatgacctacattccatccaccttggtcatccagATTCAGCTCTGATGATGCTAAGGAGGTAGTCCATTACCAAACAATCTCACCAAAGAGCTTAGCTAAATCTGTTCTCGAGGAAGGTGGCTGGTCAAACTTC

upper sequence: LOC_Os12g03060.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G017941_T01 (Zea mays), 3'ss of exon 2
aaattaccagttcatatagaaaatatttgctgaccttctt--gtggttattt-taatcaaagtttagttgtataaattacattttatttacct-tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTG
  || || | |  || |||   |  ||     | ||  ||  |   | || | | | |  | |||  | | ||||  ||||||   | | ||  ||  | ||||||||   ||||||||  |||| ||  | ||| | ||||| ||| | || ||||||| |||||  ||||||||||||||||||||||| ||||||| ||| 
--atgacaaat--atttagcgtaccttcaaataactgtttaagcaataatatatgagcttactttcctagaataacctacattccgtctgcccctgtcctccagATTCCGCTCTGATGATGCTAAGGAGGTAGTCCATTATCAAACAATCTCACCAAAGAACTTAGCTAAATCTGTTCTTGAGGAAGGTGGCTGGTCAACCTTT

upper sequence: LOC_Os12g03060.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G179737_T02 (Zea mays), 3'ss of exon 2
aaattaccagttcatatagaaaatatttgctgaccttcttgtggttattttaatcaaagtttagttgtataaattacattttatttaccttgctcg-ccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTG
 | |||      | |  |     |||||    |   |     |  ||| |  | |  | | |  | |||| |  ||||||  ||  || ||| ||  ||||||||   ||||||||  |||| ||  | ||| | || || ||| | || |||||||||||||  ||||||||||| ||||||||||| ||||||||||| 
tatttattgtacctttaaatggttatttaagcaagattgcaagaatatat-gaccttactgtcctagtatgacctacattccatccactttggtcctccagATTCAGCTCTGATGATGCTAAGGAGGTAGTCCATTACCAAACAATCTCACCAAAGAGCTTAGCTAAATCTGTTCTCGAGGAAGGTGGCTGGTCAAACTTC

upper sequence: LOC_Os12g03060.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G080404_T01 (Zea mays), 3'ss of exon 1
aaattaccagttcatatagaaaatatttgctg-accttcttgtggttattttaatcaaagttta-------gttgt------ataaattacattttatttaccttgctcg-ccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTG
               ||   ||||||||  || |||||    ||||||||| |   | | | ||         |||      || |  ||||||  ||  |||||| ||  ||||||||   ||||||||  |||| ||  | ||| | || || ||| | ||  ||||||||||||  ||||||||||| ||||||||||| ||||||||||| 
---------------atgacaaatatttattgtacctttaaatggttatttaagcaagaatatatgagcttactgtcctagaatgacctacattccatccaccttggtcatccagATTCAGCTCTGATGATGCTAAGGAGGTAGTCCATTACCAAACAATCTCATCAAAGAGCTTAGCTAAATCTGTTCTCGAGGAAGGTGGCTGGTCAAACTTC

upper sequence: LOC_Os12g03060.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G371679_T01 (Zea mays), 3'ss of exon 3
aaattaccagttcatatagaaaatatttgctg-accttcttgtggttattttaatcaaagttta-------gttgt------ataaattacattttatttaccttgctcgcc-agATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTG
               ||   ||||||||  || |||||    ||||||||| |   | | | ||         |||      || |  ||||||  ||  |||||| ||  | ||||||   ||||||||  |||| ||  | ||| | || || ||| | || |||||||||||||  ||||||||||| ||||||||||| ||||||||||| 
---------------atgacaaatatttattgtacctttaaatggttatttaagcaagaatatatgagcttactgtcctagaatgacctacattccatccaccttggtcatctagATTCAGCTCTGATGATGCTAAGGAGGTAGTCCATTACCAAACAATCTCACCAAAGAGCTTAGCTAAATCTGTTCTCGAGGAAGGTGGCTGGTCAAACTTC

upper sequence: LOC_Os12g03060.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G410155_T01 (Zea mays), 3'ss of exon 1
aaattaccagttcatatagaaaatatttgctgaccttcttgtggttattt-taatcaaagtttagttgtataaattacattttatttaccttgctcg-ccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTG
  || || | |   ||| | |  | |     |   ||   |     || | | | |  | | |  | | || |  ||||||  ||  |||||| ||  ||||||||   ||||||||  |||| ||  | ||| | || || ||| | || |||||||||||||  ||||||||||| ||||||||||| ||||||||||| 
--atgacaaatatttattgtacctttaaatggttatttaagcaagaatatatgagcttactgtcatagaatgacctacattccatccaccttggtcatccagATTCAGCTCTGATGATGCTAAGGATGTAGTCCATTACCAAACAATCTCACCAAAGAGCTTAGCTAAATCTGTTCTCGAGGAAGGTGGCTGGTCAAACTTC

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|29618674|gb|CB623686.1|CB623686
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88415912|gb|CI594024.1|CI594024
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88828089|gb|CI778654.1|CI778654
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|86904894|gb|CI310687.1|CI310687
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|33653554|gb|CF276168.1|CF276168
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|58668824|gb|CK057510.1|CK057510
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88734622|gb|CI758130.1|CI758130
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88736919|gb|CI760427.1|CI760427
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88718196|gb|CI741706.1|CI741706
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88337398|gb|CI629688.1|CI629688
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|86910179|gb|CI292983.1|CI292983
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|29657293|gb|CB653568.1|CB653568
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|66920771|gb|CX107619.1|CX107619
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88356178|gb|CI627626.1|CI627626
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|25798686|gb|CA754647.1|CA754647
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88733588|gb|CI756765.1|CI756765
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88402485|gb|CI596346.1|CI596346
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|29686826|gb|CB683101.1|CB683101
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|58597158|gb|CK007686.1|CK007686
EST:     GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
EST: gi|88337316|gb|CI629606.1|CI629606
EST:     GCGGNTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGG                         ATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC
genomic: GCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCAATAACTACGGgtaacttgtt ... tgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttaatcaaagtttagttgtataaattacattttatttaccttgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTG
  ttttaat  putative branch site (score: 3)
                                      tttacctt  putative PPT
     taatcaaagtttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaattaccagttcatatagaaaatatttgctgaccttcttgtggttattttaatcaaagtttagttgtataaattacattttatttaccttgctcgccagATTCTCTTCTGATGAGACTAAAGAAATGGTCTACTATCAGACAGTATCCCCAAAGAGCTTAGTGAAATCTGTTCTTGAGGAAGGTGGTTGGTCAAACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT