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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggttcatgattttcgtggcaatttagactttattttttttatactttctaaattagatatagtctttgcatgaattgggttggatgttgtttgtgtgtttagATATCTCCACGACAGGGGCTTCTGAGAGTGCGGGAGTTCACGTTGGCGGAGATTGAGCACTTTGTTGACCCTCTAGATAAGTCTCATCCCAAGTACCCTG

Basic information

species Glycine max
transcript GLYMA08G47890.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G47890.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g32650.1 (Oryza sativa), 3'ss of exon 3
gtgggttcatgattttcgtggcaatttagact--ttatt-ttttttatactttctaaattagatatagtctttgcatgaattgggttggatgttgtttgtgtgtttagATATCTCCACGACAGGGGCTTCTGAGAGTGCGGGAGTTCACGTTGGCGGAGATTGAGCACTTTGTTGACCCTCTAGATAAGTCTCATCCCAAGTACCCTG
 |  |   |  | |   |||| |||     ||  | |||  |  |||   | | | | ||   || |     |   ||   || |    |  |  ||        ||||||||||| || || || ||||||||||| || || || || || |||||||||||||||||||| |||||    || || || || || ||||  | ||
-taaggcaa--aatggagtggtaatgggatctagtaattactaattactgtatgttacttgactaaacaacctatgtggtctgagacaaacttctttcac-----tagATATCTCCTCGCCAAGGACTTCTGAGAGTCCGAGAATTTACTTTAGCGGAGATTGAGCACTTTGTGGACCCAGAGGACAAATCCCACCCAAAGTTTCGTG

upper sequence: GLYMA08G47890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G171688_T01 (Zea mays), 3'ss of exon 3
gtgggttcatgattttcgtggcaatttagactttattttttttatactttctaaattagatatagtctttgcatgaattgggttggatgttgtttgtgtgtttagATATCTCCACGACAGGGGCTTCTGAGAGTGCGGGAGTTCACGTTGGCGGAGATTGAGCACTTTGTTGACCCTCTAGATAAGTCTCATCCCAAGTACCCTG
 |    |    ||  ||     ||||    |||||| | |   |  || ||   || |              |     | |  || |     ||| | |   ||||||||||| || || || ||| ||||||| || ||||| || || ||||| |||||||||||||| |||||    || || || ||||| ||||    ||
-taaaatgggaatggtcacattaatt--acctttatctgta--agcctgtcaccataaagccctactaaaatactctctcgactgaagcaaattttttttgctagATATCTCCCCGTCAAGGCCTTTTGAGAGTCCGTGAGTTTACTTTAGCGGAAATTGAGCACTTTGTGGACCCAGAGGACAAATCCCATCCAAAGTTTGGTG

upper sequence: GLYMA08G47890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G041797_T01 (Zea mays), 3'ss of exon 3
gtgggttcatgattttcgtggcaatttagactttattttttttatactttctaaattagatatagtctttgcatgaattgggttggatgttgtttgtgtgtttagATATCTCCACGACAGGGGCTTCTGAGAGTGCGGGAGTTCACGTTGGCGGAGATTGAGCACTTTGTTGACCCTCTAGATAAGTCTCATCCCAAGTACCCTG
        ||  ||| | |   ||   ||   ||   |     ||| || || |  ||    |  | ||  | | | |      |  ||    |||     | |||| || |||||||| || |||||  ||||||| || ||||| ||||| ||||||||||| ||||| |||||    || || || ||||| || |    ||
---tagcaatactttgcttcaaaaagcagttattggctaagcaatagttgcttagatattcctttttttaacgt-actcactacgtctggaacttg-acaatcagATCTCGCCACGACAAGGTCTTCTCCGAGTGCGTGAATTCACATTGGCAGAGATTGAGCATTTTGTGGACCCAGAGGACAAATCACATCCAAAATTTGTTG

upper sequence: GLYMA08G47890.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgggttcatgattttcgtggcaatttagactttattttttttatactttctaaattagatatagtctttgc-atgaattgggttggat--gttgtttgtgtgtt-tagATATCTCCACGACAGGGGCTTCTGAGAGTGCGGGAGTTCACGTTGGCGGAGATTGAGCACTTTGTTGACCCTCTAGATAAGTCTCATCCCAAGTACCCTG
||   |  || | |||  | |   | | |  | | ||  | | |  |||  | ||  |  | |  |||     |||  | || ||  ||  || |  | |   |   |||||||||| ||||| |||||||| ||||| || || |||||| |||| |||||||||||||| ||||| |||    ||||||| ||||| |||| | |||
gtaa-tgtattactttgcttgatgtatgggatgtcttcatctcaatcttctttaagaaattcttttctgcattatgtctgggttttaataagtagcatattactcgcagATATCTCCTCGACAAGGGCTTCTTAGAGTTCGTGAATTCACGCTGGCAGAGATTGAGCACTTCGTTGATCCTGAGAATAAGTCACATCCTAAGTTCTCTG

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|15288150|gb|BI472041.1|BI472041
EST:     ACAAGCTTCCTTTCGCTGCTGCGCAGATTGGCCAAGCGTTTAGGAATGAG                         ATATCTCCACGACAGGGGCTTCTGAGAGTGCGGGAGTTCACGTTGGCGGAG
genomic: ACAAGCTTCCTTTCGCTGCTGCGCAGATTGGCCAAGCGTTTAGGAATGAGgtgggttcat ... gtgtgtttagATATCTCCACGACAGGGGCTTCTGAGAGTGCGGGAGTTCACGTTGGCGGAG
EST: gi|16104863|gb|BI892603.1|BI892603
EST:     GTTTAGGAATGAG                         ATATCTCCACGACAGGGGCTTCTGAGAGTGCGGGAGTTCACGTTGGCGGAG
genomic: GTTTAGGAATGAGgtgggttcat ... gtgtgtttagATATCTCCACGACAGGGGCTTCTGAGAGTGCGGGAGTTCACGTTGGCGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaattagatatagtctttgcatgaattgggttggatgttgtttgtgtgtttagATATCTCCACGACAGGGGCTTCTGAGAGTGCGGGAGTTCACGTTGGCGGAGATTGAGCACTTTGTTGACCCTCTAGATAAGTCTCATCCCAAGTACCCTG
 ttctaaa  putative branch site (score: 2)
     ttagatata  TA-rich tract