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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggggctgatttgtcttctgtgttattctaatgttaatggcttatcttgtttgctttaacttgtactttctttttcagTCTTCTTTACCTGTGGAGCTAACTGAAGCAGAAACAGAATACGCTGTCAATGTTGTTAAGCATATCTTTGACAGTCATGTGGTGTTTCAGTACAACTGCA

Basic information

species Arabidopsis thaliana
transcript AT4G34450.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 14
-------------------gttaggggctgatttgtcttctgtgttattctaatgt-taatggcttatcttgtttgctttaacttgtactttctttttcagTCTTCTTTACCTGTGGAGCTAACTGAAGCAGAAACAGAATACGCTGTCAATGTTGTTAAGCATATCTTTGACAGTCATGTGGTGTTTCAGTACAACTGCA
                   |||      | || |   || | | || ||    | | || ||   ||| |  | ||  ||    |||   ||  || |||||||||   |||||||||||| |||||||| || |||||||| || || |||||||||||||| || |||||  | ||||| |||||||| ||||||||||
gttattttacttagttcttgtttcaaaattatatactttatattttctttccttatatactgtaatatgtactatgtattctgatgttgctttcttatcagTCTTCAGAACCTGTGGAGCTTACTGAAGCGGAGACAGAATATGCAGTTAATGTTGTTAAGCACATTTTTGATCGGCATGTTGTGTTTCAATACAACTGCA

upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA11G12610.1 (Glycine max), 3'ss of exon 14
-------------------gttaggggctgatttgtcttctgtgttattctaatgt-taatggcttatcttgtttgc-tttaacttgtactttctttttcagTCTTCTTTACCTGTGGAGCTAACTGAAGCAGAAACAGAATACGCTGTCAATGTTGTTAAGCATATCTTTGACAGTCATGTGGTGTTTCAGTACAACTGCA
                   |||      |  | |   || | | || ||   || | || ||   ||| |  | ||  ||    |  | ||||  ||  ||||||||   |||||||||||| ||||||||||| |||||||| || || ||||||||||| || || |||||  | ||||| |||||||| ||||||||||
gttatttgactcaattcttgtttcataattctataatttatatcttctttccatatatactgaaatatgtattatgtattccgatgttgcttttcttaccagTCTTCAGAACCTGTGGAGCTTACTGAAGCAGAGACAGAATATGCAGTTAATGTTGTTAAACACATTTTTGATCGGCATGTTGTGTTTCAATACAACTGCA

upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 14
--------gttaggggctgatttgtc--ttctgtgttattctaatgttaatggcttatcttgtttgcttta-acttgtactttctttttcagTCTTCTTTACCTGTGGAGCTAACTGAAGCAGAAACAGAATACGCTGTCAATGTTGTTAAGCATATCTTTGACAGTCATGTGGTGTTTCAGTACAACTGCA
          | |   ||| |    |  |||| | || || |   |||  |    |||||  | || | |  | ||  |  || |||  ||||| ||   ||| |||||||| |||||||| || |||||||| ||||| |||||  |||| || || ||||| || ||||| ||||| |||||||||||||
gttctttcacttgtttctgctcccacaattctatatt-ttatgtagttctttctgtatctaatgtggtatgtattttgatattttttaccagTCCTCAGCACCCGTGGAGCTCACTGAAGCTGAGACAGAATATGCTGTTAATGTCATTAAACACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCA

upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 14
--gttaggggctgatttgtcttctgtgttattctaatgttaatggcttatcttgtttgctttaacttgtactttctttt-tcagTCTTCTTTACCTGTGGAGCTAACTGAAGCAGAAACAGAATACGCTGTCAATGTTGTTAAGCATATCTTTGACAGTCATGTGGTGTTTCAGTACAACTGCA
    |      |||||   || |      ||||||   || |||   |   ||  |   | |||  |||| ||| ||||  ||||| ||   |||||||||||| |||||||| || |||||||| || || |||||  |||| || || ||||| || ||||| ||||| |||||||||||||
gttctttcacttgattctgctccgaca--attctatattttatgtagttcttttctatatctaaaatgtatttttttttaccagTCCTCAGCACCTGTGGAGCTCACTGAAGCTGAGACAGAATATGCAGTTAATGTCATTAAACACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCA

upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 14
-------------gttaggggctgatttgtcttc-tgtgttattct--aatgttaatggcttatcttgtttgctttaacttgtactttctttttcagTCTTCTTTACCTGTGGAGCTAACTGAAGCAGAAACAGAATACGCTGTCAATGTTGTTAAGCATATCTTTGACAGTCATGTGGTGTTTCAGTACAACTGCA
              ||       | ||  |   | ||   || | |  ||||||| |   | |     | | ||||   ||    ||| ||| |||||| ||   |||||| ||||| || ||||||||||||||||| ||||| |||||||| ||||| || ||||| || ||||| ||||| |||||||||||||
gtcccctgctttttttcacatacgcttcatgcacatggactaatttgaaatgttactaattcagaagttattcttt---tttcgttttatttatcagTCCTCAGCACCTGTAGAGCTGACAGAAGCAGAAACAGAATATGCTGTTAATGTTGTCAAGCACATTTTTGATAGGCATGTTGTGTTCCAGTACAACTGCA

upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S41_154V6.1 (Physcomitrella patens), 3'ss of exon 13
--------------------gttaggggctgatttgtcttctgtgttattctaatgttaatggcttatcttgtttgctttaacttgtactttctttttcagTCTTCTTTACCTGTGGAGCTAACTGAAGCAGAAACAGAATACGCTGTCAATGTTGTTAAGCATATCTTTGACAGTCATGTGGTGTTTCAGTACAACTGCA
                     || ||   | ||   |  |    |  | |  | |  | ||| ||        |  || | |||| | |  | |||  ||||| |||   ||||||||| |||| ||||||||||||||||| ||||| || ||  |||||||| | |      | ||  | || || |||| ||| || |
tgtacattgtgtgtaaggatattgggaagtcatacttagttgcaggaaatggattccttatgtctgccgaaactgactctgacttttgcact-tttgacagTCGTCTGCTCCTGTGGAGTTAACAGAAGCAGAAACAGAATATGCTGTGAACGTGATTAAGCATGTTTACTCTGGACACATCGTCTTCCAGTTCAATTGTA

upper sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: PP1S276_96V6.1 (Physcomitrella patens), 3'ss of exon 13
---------gttaggggctgatttgtcttctgtgttattctaatgttaatggcttatcttgtttgctttaacttgt-----actttc-----tttttcagTCTTCTTTACCTGTGGAGCTAACTGAAGCAGAAACAGAATACGCTGTCAATGTTGTTAAGCATATCTTTGACAGTCATGTGGTGTTTCAGTACAACTGCA
         ||   | | | ||    |   ||  || | | |      ||   ||  |||  | | |||||  |||     |||| |      | |  |||| |||   ||||||||||| || ||||||||||||||||||||||| ||||| || |||||| | |      ||||  | || || |||| ||||||||
ttcaattgtgtcgagtgtttatagcacgcatgatttgtacaagctgatatcttttgacttaatggttttaatctgtttgttacttccgaaccctgtgtagTCGTCTACTCCTGTGGAGCTGACAGAAGCAGAAACAGAATACGCTGTGAATGTGGTCAAGCATGTGTACCCTGGTCACATCGTCTTCCAGTTCAACTGCA

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|124917755|gb|EH991629.1|EH991629
EST:     CCATTCCAGAGTTTGCCGCCTTTGGAAAACTTTTCAAG                         TCTTCTTTACCTGTGGAGCTAACTGAAGCAGAAACAGAATACG
genomic: CCATTCCAGAGTTTGCCGCCTTTGGAAAACTTTTCAAGgttaggggct ... tctttttcagTCTTCTTTACCTGTGGAGCTAACTGAAGCAGAAACAGAATACG
EST: gi|125304698|gb|EL318783.1|EL318783
EST:     CCATTCCAGAGTTTGCCGCCTTTGGAAAACTTTTCAAG                         TCTTCTTTACCTGTGGAGCTAACTGAAGCAGAAACAGAATACGCTGTCAAT
genomic: CCATTCCAGAGTTTGCCGCCTTTGGAAAACTTTTCAAGgttaggggct ... tctttttcagTCTTCTTTACCTGTGGAGCTAACTGAAGCAGAAACAGAATACGCTGTCAAT
EST: gi|125218001|gb|EL232084.1|EL232084
EST:     ATTCCAGAGTTTGCCGCCTTTGGAAAACTTTTCAAG                         TCTTCTTTACCTGTGGAGCTAACT
genomic: ATTCCAGAGTTTGCCGCCTTTGGAAAACTTTTCAAGgttaggggct ... tctttttcagTCTTCTTTACCTGTGGAGCTAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctaatgttaatggcttatcttgtttgctttaacttgtactttctttttcagTCTTCTTTACCTGTGGAGCTAACTGAAGCAGAAACAGAATACGCTGTCAATGTTGTTAAGCATATCTTTGACAGTCATGTGGTGTTTCAGTACAACTGCA
                                    cttgtactttcttttt  CT-rich tract
     taatgttaat  TA-rich tract