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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttagtaatggcctccacgcctcgtcacaaaagccagtctttgaatatacagagaagggtttaattatgttaaaccatctctatctctgttgtgttggctatgtcagGGTTGCAGAGGAGGTGATCTTTGGGGATGAGAATGTGACGACTGGAGCATCAAATGATTTCATGCAGGTGTCTCGTGTGGCACGTCAAATGATTGAGAGA

Basic information

species Arabidopsis thaliana
transcript AT1G50250.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 3
gttagttagtaatggcctccacgcctcgtcacaaaagccagtctttgaatatacagagaagggtttaattatgttaaaccatct-ctatctctgttgtgttggctatgtcagGGTTGCAGAGGAGGTGATCTTTGGGGATGAGAATGTGACGACTGGAGCATCAAATGATTTCATGCAGGTGTCTCGTGTGGCACGTCAAATGATTGAGAGA
                      |  |      ||| |    | | ||  || |      |  |||   || ||  ||  | |   || | |  | |    ||| | || ||||||||| || ||||||||||||||  | || |||||||| ||||| || || || ||||| |||||||| || ||||| ||| | |||||| |||| |||
------------------gtgggttttagtg-aaatgttcatatctgcgtacatgtgctattgtt--gttgtgcaaagtcttgaactgtgtgagcttacatggtt-tg-cagGGTTGCCGAAGAGGTGATCTTTGGCCAAGAAAATGTGACAACTGGGGCCTCCAACGATTTTATGCAGGTTTCACGTGTTGCAAGACAAATGGTTGAAAGA

upper sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G126361_T03 (Zea mays), 3'ss of exon 4
gttagttagtaatggcctccacgcctcgtcacaaaagccagtctttgaatatacagagaagggtttaattatgttaaaccatctctatctctg-ttgtgttggctatgtcagGGTTGCAGAGGAGGTGATCTTTGGGGATGAGAATGTGACGACTGGAGCATCAAATGATTTCATGCAGGTGTCTCGTGTGGCACGTCAAATGATTGAGAGA
            ||  ||    || |  ||        || |  |  |  ||  |  |  |    |    || || |   |     |  | |  |  | | |  |    ||||||||| |||||||||||||||||  | || || ||||| || ||||| || || || |||||||| ||||| ||||| ||| | || ||| | || |||
-----------gtgctctttctgcatactct----gttcatttctgcatcattgactgttgctgctgcgcatattgatggactgtgagatgtaatcttatggtttgctgcagGGTTGCTGAGGAGGTGATCTTTGGCCAAGACAACGTGACAACAGGAGCTTCCAACGACTTCATGCAAGTGTCACGTGTCGCAAGGCAGATGGTCGAAAGA
















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|86070434|gb|DR366191.1|DR366191
EST:     TACAGTAGGAGCTACCTTGAGAATCAAATGGCTGTTGCACTTGGCGGAAG                         GGTTGCAGAGGAGGTGATCTTTGGGGATGAGAATGTGACGACTGGAGCATC
genomic: TACAGTAGGAGCTACCTTGAGAATCAAATGGCTGTTGCACTTGGCGGAAGgttagttagt ... gctatgtcagGGTTGCAGAGGAGGTGATCTTTGGGGATGAGAATGTGACGACTGGAGCATC
EST: gi|86087426|gb|DR383185.1|DR383185
EST:     TACAGTAGGAGCTACCTTGAGAATCAAATGGCTGTTGCACTTGGCGGAAG                         GGTTGCAGAGGAGGTGATCTTTGGGGATGAGAATGTGACGACTGGAGCATC
genomic: TACAGTAGGAGCTACCTTGAGAATCAAATGGCTGTTGCACTTGGCGGAAGgttagttagt ... gctatgtcagGGTTGCAGAGGAGGTGATCTTTGGGGATGAGAATGTGACGACTGGAGCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaagggtttaattatgttaaaccatctctatctctgttgtgttggctatgtcagGGTTGCAGAGGAGGTGATCTTTGGGGATGAGAATGTGACGACTGGAGCATCAAATGATTTCATGCAGGTGTCTCGTGTGGCACGTCAAATGATTGAGAGA
      gtttaat  putative branch site (score: 4)
       tttaattatgttaaa  TA-rich tract