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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttaagacactaaactttttttgcgatcagttctatcgtatcttcaaaagtatattattgtgagatattaaaattttgaccttttttttattcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG

Basic information

species Oryza sativa
transcript LOC_Os03g16980.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 4
cttaagacactaaactttttttgcgatcagttctatcgtatcttcaaaagtatattattgtgagatattaaa--attttg-accttttttttattcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG
   ||||  ||||    |   |||      || | |  |   |  |   ||   |  |  |||| ||   |   || ||| |  |  ||| |||   ||| |||||||||| |||| || ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||
---aagagtctaacagatcactgctgctccttttttaatcagtgtatgtgtgcttcctcatgagttaagcacttatcttgtaaatcctttctatctgttttagATGTCACCGAGCCACTTCTTGTGGAGGTTGACCAGATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAATCCTGTTAAG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 3
cttaagacactaaactttttttgcgatcagttctatcgtatcttcaaaagtatattattgtgagatattaaa--attttg-accttttttttattcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG
   |    |  | |    | ||   |   |||   |  ||  |  | | ||   |  |  |||| ||   |   ||| || |  || ||| ||||  ||| |||||||||| |||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
--cagtctaacagatcactcttctcagttgtttctttttaaata-atatgtgcctcctcatgagttaggcacttattctgtaaattctttctatttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 4
-----cttaagacactaa-actttttttgcgatcagttctatcgtatcttcaaaagtatattattgtgagatattaaaattttgaccttttttttattcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG
      |  |   | |     ||| ||||  |||||  | |       ||    |||  ||||  || ||  | | |   | | |  || ||| ||||  ||| |||||||||| |||| || |||||||| ||||||||||||| ||||||||||||||||||||||||||||||||||||||||||| |||| |||
ttttggtacaagtattgttgatttctttggaatcagaaccaattaggtttt---agttcatta--gttaggcactgattctgtaaa-ttctttctatttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTGTCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACTCTGTTAAG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 5
-----cttaagacactaa-actttttttgcgatcagttctatcgtatcttcaaaagtatattattgtgagatattaaaattttgaccttttttttattcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG
      |  |   | |     ||| ||||  |||||  | |       ||    |||  || |  || ||  | | |   | | |  || ||| | ||  ||| |||||||||| |||| || |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||| |||
ttttggtacaagtattgttgatttctttggaatcagaaccaattaggtttt---agttcatga--gttaggcactgattctgtaaa-ttctttctgtttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACTCTGTTAAG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G157772_T02 (Zea mays), 3'ss of exon 1
--ctta-agacactaaactttttttgcgatcagttctatcgtatcttcaaaagtatattattgtgagatattaaaattttgaccttttttttattcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG
  | || || || |    ||  |  |   || |||  || | || |||     | |  | ||    ||   |  | | |  |  || ||| ||||  ||| |||||||| | |||| || ||||| || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
atcatatagtcaatgtgtttcctgagttgtctgttgaat-gaattttctttcttctgctcttaattgaccatttactgtaaa--ttctttctatttgttttagATGTCATCGAGCCGCTTCTTGTAGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTTAAG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 10
-----cttaagacactaa-actttttttgcgatcagttctatcgtatcttcaaaagtatattattgtgagatattaaaattttgaccttttttttattcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG
      |  |   | |     ||| ||||  |||||  | |       ||    |||  || |  || ||  | | |   | | |  || ||| ||||  ||| |||||||||| |||| || |||||||| ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| |||| |||
ttttggtacaagtattgttgatttctttggaatcagaaccaattaggtttt---agttcatga--gttaggcactgattctgtaaa-ttctttctatttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATATTCTACAAGCACAACTCTGTTAAG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
--cttaagac-actaaactttttttgcgatcagttctatcgtatcttcaaaagtatattattgtgagatattaaaattt-tgaccttttttttattcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG
  | ||| |  | | |   | |   | |   ||||     |  | || | | || | ||| | |     ||||||||   ||  ||||| |||   |    ||||||||||  |||   || |  | |||||||| ||||||||||| ||||| ||||||||||| ||||||||||||||  |||||||||| |||
aacataacatgaatgattctatcaggtgcagagtttctctgcgtttttagatgtgttttaattta----attaaaatgcatgtacttttcttttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 3
--cttaagac-actaaactttttttgcgatcagttctatcgtatcttcaaaagtatattattgtgagatattaaaattttgaccttttttttattcattt-cagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG
  | | | |  | | |   | |  || |   |||| |   || | || | | |  |  || | |     ||||||||    |   |||| || | | |   ||||||||||  |||   || |  | |||||||| ||||||||||| ||||| ||||| ||||| ||||| ||||||||  |||||||||| |||
aacatgacatgaatgatgctatcatgtgcatagtttttctgtgtttttagatgcgttgtaattta----attaaaatgcatatacttttattttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCAGCTTCTCCAATTTTCTACAAATACAACCCTGTAAAG

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 4
cttaagacactaaactttttttgcg-atcagttctatcgtatcttcaaaagtatattattgtgagatattaaaattttgaccttttttttattcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG--------
  || |    | || || | | ||   |   | |||| |    |  || | |    | || ||   |||    ||||  |  ||  ||||     |  ||||||||||  |||| ||  |  | |||||||| || || || || ||||| || |||||||| || |||||||||||| |||||||||| |||        
-gtatggttttgaaattctctggcttgttgctgctattgagaatggaatattcctgtcttttgttctatcc--atttatattttggttttgggtttaacagATGTCACGGAGCCACTTTTGATCGAGGTTGATCAGATTTACCATCTTGCATGTCCTGCTTCTCCTATCTTCTACAAGTACAACCCTGTGAAGACAATCAA

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|29668686|gb|CB664961.1|CB664961
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|58659240|gb|CK047920.1|CK047920
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|313080404|gb|HO213412.1|HO213412
EST:     CAATCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|33675428|gb|CF303667.1|CF303667
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|428184|gb|D24332.1|D24332
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|30229035|gb|CB966926.1|CB966926
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|30228342|gb|CB966233.1|CB966233
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|29668646|gb|CB664921.1|CB664921
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|58672962|gb|CK061648.1|CK061648
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|33680606|gb|CF308845.1|CF308845
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|58654932|gb|CK043612.1|CK043612
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|58590735|gb|CF989043.1|CF989043
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|33380802|gb|CF196145.1|CF196145
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|58656016|gb|CK044696.1|CK044696
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGGGTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|58659773|gb|CK048453.1|CK048453
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|30226636|gb|CB964528.1|CB964528
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagtatattattgtgagatattaaaattttgaccttttttttattcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG
                            ttttgac  putative branch site (score: 3)
                                  ccttttttttattcat  CT-rich tract
                 agatattaaaattttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttaagacactaaactttttttgcgatcagttctatcgtatcttcaaaagtatattattgtgagatattaaaattttgaccttttttttattcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG

- - - -cactaaa
- - - - - - - - -tttttgc
- - - - - - - - - - - - - - - - - - - - - - caaaagta