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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctactaataacactattatttacaaagttgtaccatgagctgttcctccaactaaaaatttccatgagttaagttaatgttaacttgtttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATTTTTCCAAACTAAAAAGGACTGTGACAAGGTCACTCGTCAACTTAGAATG

Basic information

species Oryza sativa
transcript LOC_Os01g68320.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68320.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G362850_T01 (Zea mays), 3'ss of exon 8
gtatctactaataaca--ctattatttacaaagttgtaccatgagctgtt------cctccaactaaaaatttccatgagttaagttaatgttaacttgtttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATTTTTCCAAACTAAAAAGGACTGTGACAAGGTCACTCGTCAACTTAGAATG
|||| ||    | ||   || ||   || ||| || ||   | |  |  |      | | | | || ||||   || |   | |||| || || || | ||||  ||||||||||||| || || ||||||||||||||||| ||| | ||||||||||| |||||||| |||||||| || || ||| |||| || || |||||||||
gtatgtatggttgacggtcttttgactaaaaacttttatgctcacttactatgctactttcgattacaaatggacacggtgtgagttgattttcacctctttcccacagACTCAGTAAGCTCTTGTCTGATCTAATGGATGGGAGCCGTATCTTGATATTCTTCCAAACAAAAAAGGATTGCGATAAGATCACCCGGCAGCTTAGAATG
















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|29661778|gb|CB658053.1|CB658053
EST:     AGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: AGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29664446|gb|CB660721.1|CB660721
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29633338|gb|CB638347.1|CB638347
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|88417599|gb|CI581622.1|CI581622
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCC-AG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29629642|gb|CB634651.1|CB634651
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|218485924|gb|FG959170.1|FG959170
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTT-ATCTGATCTAATGGATG-AAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29678103|gb|CB674378.1|CB674378
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTANACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29633337|gb|CB638346.1|CB638346
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29662446|gb|CB658721.1|CB658721
EST:     TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: TCCATACAGCAAATTATTGAGGTCATATCTGAACACGAAAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
EST: gi|29669297|gb|CB665572.1|CB665572
EST:     AAAGTATCCCAG                         ACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT
genomic: AAAGTATCCCAGgtatctacta ... tttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctccaactaaaaatttccatgagttaagttaatgttaacttgtttcttacagACTCAGTAAACTTTTATCTGATCTAATGGATGGAAGCAGAATCTTGATATTTTTCCAAACTAAAAAGGACTGTGACAAGGTCACTCGTCAACTTAGAATG
                                   tgttaac  putative branch site (score: 2)
                                         cttgtttctt  CT-rich tract
                          ttaagttaatgttaa  TA-rich tract