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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactacacaatttcttaaccatcaaacatcggttggtctaaagacctttgatattgatttaccatattgcgtaatccagGTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGTGTCCATGGAGCTGCACTTGGCGAGAAGGAAGTTGAGGCTACCAGAAATA

Basic information

species Arabidopsis thaliana
transcript AT3G60750.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 4
----gtaactacacaatttcttaaccatcaaacatcggttggtctaaagacctttgatattgatttaccatattgcgtaatccagGTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGTGTCCATGGAGCTGCACTTGGCGAGAAGGAAGTTGAGGCTACCAGAAATA
    ||  ||     || |   |||| | |    |   | | | |  |    | | || ||| | ||   |||  |    |  |||| ||||| || || |||| ||| |||||||||||||| |||||||||||||| ||||||  |||||| || |  || || ||||| || |||||  | |
gttggtttcttttgtatctgc-aacctttatgtttttttcgctgtggat-tttataatgttggtctaatttat-actccttttagGTGACTACCACGATCGGTTTTGGATCTCCCAACAAGGCCAACTCATACAGTGTTCATGGAAGTGCACTGGGTGCCAAAGAGGTTGAAGCAACCAGGCAGA

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 4
---------gtaactacaca----atttcttaaccatcaaacatcggttggtc---taaagacctttgatattgatttaccatattgcgtaatc---cagGTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGTGTCCATGGAGCTGCACTTGGCGAGAAGGAAGTTGAGGCTACCAGAAATA
         | |  || |      |  ||  ||   | ||  || |||  ||    |||       || | |   |||  |  | |   | ||    |||||||| || |||||||||||||| ||||| |||||||| ||||| |||||||| ||||||  |||||| || |  || |||||||| || |||||  | |
gagaaactggaagttataggtgggaaatcaaaatagtaaattatgggtcagtttattaagtgtagctggtttgtcttttgctaactctatcatttcacagGTCACAACAACCATTGGTTATGGTTCTCCTAACAAGGCTAACTCCTACAGTGTGCATGGAAGTGCACTGGGTGCCAAAGAAGTTGATGCCACCAGGCAGA

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------------------------------------------------------------gtaactacacaatttcttaaccatcaaacatcggttg-gtctaaagacctttgatattgatttaccatattgcgtaatccagGTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGTGTCCATGGAGCTGCACTTGGCGAGAAGGAAGTTGAGGCTACCAGAAATA
                                                                                                               | || || || |||| |||      |    | ||  |  | | |  | |||| || || || |   || |    |    ||||| || ||||||||||| | ||| ||||| |||||||| ||||| |||||||| ||||||  |||| | ||    || ||||| || ||||| || || |
gttagttacatgaactgaatattgaagcaaattgatttatccaaaacatcatttacgtcactagttacttgagtatactagtggaagtagcataatgtgatttctgtgagcgaaagtaaaccattt-ttatttgctatttttggggggtattttatcagcttt-atgttcatctgtgat-tactatttcacagGTAACCACTACCATTGGATTTGGTTCTCCAAACAAGGCTAACTCCTACAGTGTTCATGGAAGTGCATTAGGTACTAAAGAAGTGGATGCTACAAGGAAGA

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 4
-------------gtaactacaca-atttcttaaccatcaaacatcggttggtctaaagacctttgatattgatttacca-------tattgcgtaatccagGTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGTGTCCATGGAGCTGCACTTGGCGAGAAGGAAGTTGAGGCTACCAGAAATA
             ||   || ||| | |  | ||  ||      |  |||    |  | |||  || |||   ||| | |       |||| | |    ||||| ||||| |||||||||||||| || || |||||| | |||||||||||||| ||||||  |||||| ||    |||||  | || || || || || |
cttcattcaagttgtttttagacacaatattaaattattggg--tttgttctcttccaaaccagtgctatccttttgctaacttttatattacctttaacagGTGACTACAACCATTGGTTATGGATCCCCAAACAAGTCAAACTCATACAGTGTACATGGAAGTGCACTAGGTCCTAAGGAGTTGGATGCCACAAGGAAGA

upper sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv16s0022g01440.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------gtaactacacaatttcttaaccatcaaacatcggttggtctaaagacctttgatattgatttaccatattgcg----taatccagGTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGTGTCCATGGAGCTGCACTTGGCGAGAAGGAAGTTGAGGCTACCAGAAATA
                              |    |    | |||  |   |     | |       | |   ||  || ||  ||   |    | | | |     | || ||||| || ||||||||||||||||| ||||| |||||||| |||||||| ||||| |||||   |||| | || |  || ||||| || || || || || |
gtcatttctccaacatgatctttaaggttttggtcaagagagttccaacttaaacttcttttcccccttttctgaagttggactttacctctataaacttctctgtttatgcagGTGACAACTACCATTGGTTATGGTTCTCCTAACAAGGCAAACTCATATAGTGTTCATGGGAGTGCATTGGGTGCTAAAGAAGTAGATGCAACAAGGAAGA

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|125242574|gb|EL256659.1|EL256659
EST:     CTGCCATTAAGGAAGCTAAAACTGTTACTGACAAGCCTACTTTGATCAAG                         GTCACTACTACCA
genomic: CTGCCATTAAGGAAGCTAAAACTGTTACTGACAAGCCTACTTTGATCAAGgtaactacac ... cgtaatccagGTCACTACTACCA
EST: gi|86072919|gb|DR368676.1|DR368676
EST:     CTGCCATTAAGGAAGCTAAAACTGTTACTGACAAGCCTACTTTGATCAAG                         GTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGT
genomic: CTGCCATTAAGGAAGCTAAAACTGTTACTGACAAGCCTACTTTGATCAAGgtaactacac ... cgtaatccagGTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGT
EST: gi|125025721|gb|EL097990.1|EL097990
EST:     CTGCCATTAAGGAAGCTAAAACTGTTACTGACAAGCCTACTTTGATCAAG                         GTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCG
genomic: CTGCCATTAAGGAAGCTAAAACTGTTACTGACAAGCCTACTTTGATCAAGgtaactacac ... cgtaatccagGTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCG
EST: gi|125154551|gb|EL185124.1|EL185124
EST:     CTGCCATTAAGGAAGCTAAAACTGTTACTGACAAGCCTACTTTGATCAAG                         GTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCA
genomic: CTGCCATTAAGGAAGCTAAAACTGTTACTGACAAGCCTACTTTGATCAAGgtaactacac ... cgtaatccagGTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCA
EST: gi|125157296|gb|EL186470.1|EL186470
EST:     CTGCCATTAAGGAAGCTAAAACTGTTACTGACAAGCCTACTTTGATCAAG                         GTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGT
genomic: CTGCCATTAAGGAAGCTAAAACTGTTACTGACAAGCCTACTTTGATCAAGgtaactacac ... cgtaatccagGTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGT
EST: gi|124993551|gb|EL065820.1|EL065820
EST:     CTGCCATTAAGGAAGCTAAAACTGTTACTGACAAGCCTACTTTGATCAAG                         GTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGT
genomic: CTGCCATTAAGGAAGCTAAAACTGTTACTGACAAGCCTACTTTGATCAAGgtaactacac ... cgtaatccagGTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGT
EST: gi|124795403|gb|EH885082.1|EH885082
EST:     ACTTTGATCAAG                         GTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGT
genomic: ACTTTGATCAAGgtaactacac ... cgtaatccagGTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacatcggttggtctaaagacctttgatattgatttaccatattgcgtaatccagGTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGTGTCCATGGAGCTGCACTTGGCGAGAAGGAAGTTGAGGCTACCAGAAATA
                           tattgat  putative branch site (score: 3)
                      tttgatattgattta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactacacaatttcttaaccatcaaacatcggttggtctaaagacctttgatattgatttaccatattgcgtaatccagGTCACTACTACCATTGGTTATGGGTCTCCCAACAAGGCGAACTCATACAGTGTCCATGGAGCTGCACTTGGCGAGAAGGAAGTTGAGGCTACCAGAAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA