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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagacacctactaaagctatcattttgctcctgaaacttaacaatttgtctgttgctaaaagaaattgcttggttggtgtgcagCTATCTAGCTCCCGAATATGCTCAAAGCGGGCAAATCACAGAAAAAGCTGATGTCTACTCGTTCGGGGTTGTTCTAGTTGAGCTAGTCACTGGCCGCAAA

Basic information

species Arabidopsis thaliana
transcript AT3G13690.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13690.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g41870.1 (Oryza sativa), 3'ss of exon 7
gtgagacacctactaaagctatcattttgctcctgaaac--ttaacaattt--gtctgttgctaa-aagaaattgcttggttggtgtgcagCTATCTAGCTCCCGAATATGCTCAAAGCGGGCAAATCACAGAAAAAGCTGATGTCTACTCGTTCGGGGTTGTTCTAGTTGAGCTAGTCACTGGCCGCAAA
       |  || | |   |  ||  |   |  || |||  |   || |||  | |  ||  |||  ||    ||||||| || | ||||| ||||| || || ||||| || || || || ||||| ||||| ||||||||||| ||||| || ||||||||  ||||||| || |||||||| ||||| 
-----gtaaatattgagatttgcaactgtgtgttgtaaccatgtgcagttttgggcacttattaacgaggctctgcttggctg-tctgcagTTATCTGGCACCAGAATACGCACAGAGTGGACAAATAACAGAGAAAGCTGATGTATACTCTTTTGGGGTTGTGTTAGTTGAACTTGTCACTGGGCGCAAG

upper sequence: AT3G13690.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G480607_T04 (Zea mays), 3'ss of exon 6
----gtgagacacctactaaagctatcattttgctcctgaaacttaacaatttgtctgttgctaaaagaaattgcttggttggtgtgcagCTATCTAGCTCCCGAATATGCTCAAAGCGGGCAAATCACAGAAAAAGCTGATGTCTACTCGTTCGGGGTTGTTCTAGTTGAGCTAGTCACTGGCCGCAAA
    ||   |   ||| |  |   ||  |||       |  | ||||   ||||  | | |||||    |  |   |   || | ||||||||||| ||||| |||||||| || || |||||||| ||||| || |||||||| ||||| |||||||||||  |||| || || |||||||| || || 
gtgggttttaatactattctatgaatattttcatcataggcaattaaacttttgagtttagctaacgacagctttattactg-tctgcagCTATCTGGCTCCTGAATATGCACAGAGTGGGCAAATAACAGAGAAGGCTGATGTATACTCTTTCGGGGTTGTGTTAGTGGAACTTGTCACTGGGCGGAAG

upper sequence: AT3G13690.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G142068_T01 (Zea mays), 3'ss of exon 6
gtgagacacctactaaagctatcattttgctcctgaaacttaacaatttg----tctgttgctaaaagaaattgcttggttggtgtgcagCTATCTAGCTCCCGAATATGCTCAAAGCGGGCAAATCACAGAAAAAGCTGATGTCTACTCGTTCGGGGTTGTTCTAGTTGAGCTAGTCACTGGCCGCAAA
|| ||    |  |   ||||| | |  | |      | | ||  | ||||    || |   ||         |  |   |   || |||||||||| || ||||| |||||||| || |||||||| || || || || ||||||||||||||||||||||| ||||| || || || ||||| || || 
gtaagtttgcagcgctagctagcttggtccggtatgaccgtatgagtttgcaaatccgagcctgtgtttttcttatgtatatatgcgcagCTATCTGGCGCCCGAGTATGCTCAGAGTGGGCAAATAACGGAGAAGGCAGATGTCTACTCGTTCGGGGTTGTACTAGTGGAACTTGTAACTGGACGGAAG

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|116452044|gb|EG494636.1|EG494636
EST:     CAGCCTGATGGGGAAATGGGTGTAGATACACGAGTGATAGGAACCTTCGG                         CTATCTAGCTCCCGAATATGCTCAAAGCGGGCAAATCACAGAAAAAGCTGA
genomic: CAGCCTGATGGGGAAATGGGTGTAGATACACGAGTGATAGGAACCTTCGGgtgagacacc ... tggtgtgcagCTATCTAGCTCCCGAATATGCTCAAAGCGGGCAAATCACAGAAAAAGCTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgaaacttaacaatttgtctgttgctaaaagaaattgcttggttggtgtgcagCTATCTAGCTCCCGAATATGCTCAAAGCGGGCAAATCACAGAAAAAGCTGATGTCTACTCGTTCGGGGTTGTTCTAGTTGAGCTAGTCACTGGCCGCAAA
                        tgctaaa  putative branch site (score: 2)
                           taaaagaaatt  TA-rich tract