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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_Os03g16980.5
intron # 4
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|58654932|gb|CK043612.1|CK043612
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|58659240|gb|CK047920.1|CK047920
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|58590735|gb|CF989043.1|CF989043
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|30229035|gb|CB966926.1|CB966926
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|428184|gb|D24332.1|D24332
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|30228342|gb|CB966233.1|CB966233
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|313080404|gb|HO213412.1|HO213412
EST:     CAATCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         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|58672962|gb|CK061648.1|CK061648
EST:     CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATG                         ATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctac ... ttcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTT
EST: gi|58659773|gb|CK048453.1|CK048453
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