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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatttgggctaatagttatttgagctaatacctccatctatgctagtcattagtgtgattatgcaattctaattgctgaacttttggtgctgccttcttagGTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCAACTGGAGTTTATAGCTACAGAGGTTGTGATGCAAATATTCCTGCCTCAA

Basic information

species Oryza sativa
transcript LOC_Os01g63870.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63870.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G095611_T01 (Zea mays), 3'ss of exon 6
gtaagatttgggctaat--agttat----ttgagctaatacctccatctatgctagtcattagtgtgattatgcaattctaattgctgaacttttggtgctgccttcttagGTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCAACTGGAGTTTATAGCTACAGAGGTTGTGATGCAAATATTCCTGCCTCAA
|||||||||   || ||  ||||||    ||||   |||   |  |||| ||||      | || |||| |||  |  |||||| |||||||  || ||||||||  ||||||||||||||   |||| |||||||||||| | ||||| ||||| ||||||||||||||||||||||||| |||||||||||||||||||||||||||||
gtaagattttctcttatgaagttatgatgttgattgaatgtgtggatctgtgctgcatgctggt-tgat-atgagaggctaatttctgaactactgatgctgcctctttagGTTCCTCTTGGATTAGGAATCACATGGGCTGTTGCTTTCGTTCTCACAGCAACTGGAGTTTATAGCTACAAAGGTTGTGATGCAAATATTCCTGCCTCAA

upper sequence: LOC_Os01g63870.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G09060.1 (Glycine max), 3'ss of exon 6
gtaagatttgggctaatagttatttgagctaatacctccatctatgctagtcattagtgtgattatgcaattctaattgctgaacttttggtgctgccttcttagGTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCAACTGGAGTTTATAGCTACAGAGGTTGTGATGCAAATATTCCTGCCTCAA
||||| ||     | | | |   ||    || |  || ||    |   | | |    |||| |   |||| |   ||| |||   |||     |     |  ||||||||||| | ||| |  || ||||||||  | |||||  | || || | | | |||||||| ||||||| ||| |||||||||||||| ||| ||||||
gtaag-ttgaacattacaatatcttacattact--cttcagtagttgaaataaaatttgtggtgtagcaaat--gatttctg--ttttcatcacctaactgctagGTTCCTCTGGGTCTGGCAATTACATGGGCATTTGCTTTCATGCTGACTGAAGCAGGAGTTTACAGCTACAAAGGGTGTGATGCAAATATACCTTCCTCAA
















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|58659627|gb|CK048307.1|CK048307
EST:     ACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG                         GTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCA
genomic: ACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCGgtaagatttg ... gccttcttagGTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCA
EST: gi|58658393|gb|CK047073.1|CK047073
EST:     ACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG                         GTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCA
genomic: ACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCGgtaagatttg ... gccttcttagGTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCA
EST: gi|58652789|gb|CK041469.1|CK041469
EST:     ACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG                         GTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCA
genomic: ACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCGgtaagatttg ... gccttcttagGTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCA
EST: gi|58654749|gb|CK043429.1|CK043429
EST:     ACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG                         GTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCA
genomic: ACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCGgtaagatttg ... gccttcttagGTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCA
EST: gi|58656604|gb|CK045284.1|CK045284
EST:     ACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG                         GTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCA
genomic: ACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCGgtaagatttg ... gccttcttagGTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCA
EST: gi|58655477|gb|CK044157.1|CK044157
EST:     ACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCG                         GTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCA
genomic: ACCTCCGAAAAGTAAAGTTATTTGGCTACCGGGTGTTTTTAATTTATGCGgtaagatttg ... gccttcttagGTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattagtgtgattatgcaattctaattgctgaacttttggtgctgccttcttagGTTCCTCTTGCTCTAGGGATCACATGGGCTATCGCTTTTGTTCTAACAGCAACTGGAGTTTATAGCTACAGAGGTTGTGATGCAAATATTCCTGCCTCAA
                    ttctaat  putative branch site (score: 2)
                                           ctgccttctt  putative PPT
                  aattctaatt  TA-rich tract