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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagagaactcgtatcgattattggttacagtaagtgcattgtgttgtatacaaactatttcctaatggtgttcacatgtgggtttagGTTAGCAAACCTCTTCTGGAGACATCAAGGAAAGGCTATCTCGCTGCTATCTCTGCTTCGAGTTACTCCTTTGTTTCCTTGCTGAGGCATTTTCTGCCAA

Basic information

species Arabidopsis thaliana
transcript AT2G05990.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G05990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G125052_T01 (Zea mays), 3'ss of exon 5
-----gtagagaactcg--tatcgattattggttacagtaagtgcattgtg--------ttgt-atacaaactatttcctaatggtgtt------cacatgtgggttt--agGTTAGCAAACCTCTTCTGGAGACATCAAGGAAAGGCTATCTCGCTGCTATCTCTGCTTCGAGTTACTCCTTTGTTTCCTTGCTGAGGCATTTTCTGCCAA
      ||  | |||||  | |  ||   ||  | |||   |||   ||          |||| | ||     |||  ||||   | ||      |||||||   |||  |||| |  |||||| |  ||||||||||||| | ||||||||| || || || || || ||||||||||||| |||||| |||||   |||||| || || |
gtacaatatcgcactcgcctgtgtatatgtgtgtgcagcgggtgtggtgcagcttttgcttgtgacactgtacattgtctaaccatcttaaaaaccacatgtcattttgaagGTAACAAAACCTTTGTTGGAGACATCAAGAAGAGGCTATCTTGCGGCAATTTCAGCATCGAGTTACTCCTATGTTTCATTGCTTCAGCATTTCCTTCCTA

upper sequence: AT2G05990.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0007g06390.t01 (Vitis vinifera), 3'ss of exon 7
----------gtagagaactcgtatcgattattggttacagtaagtgcattgtgttgtatacaaactatttcctaatggtgttcacatgtgggtttagGTTAGCAAACCTCTTCTGGAGACATCAAGGAAAGGCTATCTCGCTGCTATCTCTGCTTCGAGTTACTCCTTTGTTTCCTTGCTGAGGCATTTTCTGCCAA
           |     | || |||   || ||||||   ||   |   |     ||  |        ||  | ||      |  |||        |||| | |||||| || |||||||||||||| || || ||||| || ||||| ||||| || ||||| ||||||||||| ||||| | |||||| || ||||
gtcttttccaatttgacattcttat--gtttttggtttatgtttttctttcaccctg-gtctccgtatttagccaacaaaaattccataca----cagGTCACCAAACCACTCCTGGAGACATCAAGAAAGGGATATCTTGCAGCTATTTCTGCATCAAGTTATTCCTTTGTTTCTTTGCTCAAGCATTTCCTCCCAA
















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|164000598|gb|ES146557.1|ES146557
EST:     GCAAATGGTCCAGAG                         GTTAGCAAACCTCTTCTGGAGACATCAAGGAAAGGCTATCTCGCTGCTATC
genomic: GCAAATGGCCCAGAGgtagagaact ... gtgggtttagGTTAGCAAACCTCTTCTGGAGACATCAAGGAAAGGCTATCTCGCTGCTATC
EST: gi|47829300|gb|CK118984.1|CK118984
EST:     ATTTTGGAAGCATTGACATTCTTGTCCATTCCCTTGCAAATGGCCCAGAG                         GTTAGCAAACCTCTTCTGGAGACATCAAGGAAAGGCTATCTCGCTGCTATC
genomic: ATTTTGGAAGCATTGACATTCTTGTCCATTCCCTTGCAAATGGCCCAGAGgtagagaact ... gtgggtttagGTTAGCAAACCTCTTCTGGAGACATCAAGGAAAGGCTATCTCGCTGCTATC
EST: gi|124788998|gb|EH878677.1|EH878677
EST:     ATTTTGGAAGCATTGACATTCTTGTCCATTCCCTTGCAAATGGCCCAGAG                         GTTAGCAAACCTCTTCTGGAG
genomic: ATTTTGGAAGCATTGACATTCTTGTCCATTCCCTTGCAAATGGCCCAGAGgtagagaact ... gtgggtttagGTTAGCAAACCTCTTCTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgcattgtgttgtatacaaactatttcctaatggtgttcacatgtgggtttagGTTAGCAAACCTCTTCTGGAGACATCAAGGAAAGGCTATCTCGCTGCTATCTCTGCTTCGAGTTACTCCTTTGTTTCCTTGCTGAGGCATTTTCTGCCAA
                           tcctaat  putative branch site (score: 2)
              tatacaaactattt  TA-rich tract