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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATAACATTTGGGTTAATGTTGATGTTCTTATGACTCATGATGTTTGTGGTCCTGGTGCTTTTGGTATCTTCAAGAGAGAGTTTGGTGAAAAAGCCAAGgtacgtattcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttctgtaattatacaaattgagaagagttttgataggtttagtttaggtattagtgaattggtgatcacaatggttgtttagtgtaacttattgtgattgtttacttacttgctgaag

Basic information

species Arabidopsis thaliana
transcript AT4G13430.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA17G37540.1 (Glycine max), 5'ss of exon 3
-TGATAACATTTGGGTTAATGTTGATGTTCTTATGACTCATGATGTTTGTGGTCCTGGTGCTTTTGGTATCTTCAAGAGAGAGTTTGGTGAAAAAGCCAAGgtacgtattcttcttcttcttctt--cttcttcttcttcttcttcttcttcttcttct-tcttcttcttcttcttcttctgtaattatacaaattgagaagagttttgataggtttagtttaggtattagtgaattggtgatcacaatggttgtttagtgtaacttattgtgattgtttacttacttgctgaag
  |||||  ||||||| ||||||||| || | ||||| |||||||| ||||| |||||| || |||| || |||||||| |||||||||||  | ||||||||| || | ||  || |  |  ||  || ||  | ||||    |||  || ||    | | ||  | || ||||  | || |    |||   |||                                                                                                   
GCGATAATGTTTGGGTCAATGTTGATATTTTGATGACACATGATGTGTGTGGCCCTGGTTCTATTGGGATTTTCAAGAGGGAGTTTGGTGACGATGCCAAggtaagtttgctaattgtcttaattggctgctgttacttcggactctcttttttagggtgttttgatatttttctgatgctttgtggatatgcattccat-----------------------------------------------------------------------------------------------

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 5'ss of exon 3
TGATAACATTTGGGTTAATGTTGATGTTCTTATGACTCATGATGTTTGTGGTCCTGGTGCTTTTGGTATCTTCAAGAGAGAGTTTGGTGAAAAAGCCAAGgtacgtattcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttctgtaattatacaaattgagaagagttttgataggtttagtttaggtattagtgaattggtgatcacaatggttgtttagtgtaacttattgtgattgtttacttacttgctgaag
||| ||  | ||||| ||||||||| |  | ||||| |||||||| ||||| || ||| ||||||| |||||||||| |||||||||||| || || ||||||  |||   |   | |    |   |  | |  |||||  |  || ||    |       ||||  || || ||  |  || ||  |  |||   || ||||                                                                                        
TGAGAATGTATGGGTAAATGTTGATCTCTTGATGACCCATGATGTCTGTGGCCCAGGTTCTTTTGGAATCTTCAAGAAAGAGTTTGGTGAGAATGCAAAGgtatatatgtgttaacatgcaatgagttgt-tgattcttacttgtcatccaaataggaagattctaatt-ttgttgaggcatcatttag-ttgcttagcgttt----------------------------------------------------------------------------------------

upper sequence: AT4G13430.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S227_66V6.1 (Physcomitrella patens), 5'ss of exon 3
TGATAACATTTGGGTTAATGTTGATGTTCTTATGACTCATGATGTTTGTGGTCCTGGTGCTTTTGGTATCTTCAAGAGAGAGTTTGGTGAAAAAGCCAAGgtacgtattcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttctgtaattatacaaattgagaagagttttgataggtttagtttaggtattagtgaattggtgatcacaatggttgtttagtgtaacttattgtgattgtttacttacttgctgaag
 || ||  | ||||| || |  |||||||| |||||||||||||||||||| |||||  |  ||||||||||||||| ||| || ||| |||| || |||||| ||    |     |  |  |   |       || ||     | |   |||      ||     |         || || | |  |  |  |  || |                                                                                           
AGAGAATGTGTGGGTGAAGGCAGATGTTCTCATGACTCATGATGTTTGTGGCCCTGGAACCATTGGTATCTTCAAGAAAGAATTCGGTCAAAATGCTAAGgtatgttacttgagcatggtggtaacttaagcgattatttgagatttgtctctctcgtatcaatgaccgacatacgtgcaactgtcaacctcaattaggg-------------------------------------------------------------------------------------------

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|124939662|gb|EL016185.1|EL016185
EST:     GTCCTGGTGCTTTTGGTATCTTCAAGAGAGAGTTTGGTGAAAA-GCCAAG                         GTTTGGGATCCGGAGAAGATTGTTGT
genomic: GTCCTGGTGCTTTTGGTATCTTCAAGAGAGAGTTTGGTGAAAAAGCCAAGgtacgtattc ... cttgctgaagGTTTGGGATCCGGAGAAGATTGTTGT
EST: gi|124731144|gb|EH822546.1|EH822546
EST:     GTCCTGGTGCTTTTGGTATCTTCAAGAGAGAGTTTGGTGAAAAAGCCAAG                         GTTTGGGATCCGGAGAAGATTGTTGTGATTCCGGAT
genomic: GTCCTGGTGCTTTTGGTATCTTCAAGAGAGAGTTTGGTGAAAAAGCCAAGgtacgtattc ... cttgctgaagGTTTGGGATCCGGAGAAGATTGTTGTGATTCCGGAT
EST: gi|124714519|gb|EH805921.1|EH805921
EST:     GTCCTGGTGCTTTTGGTATCTTCAAGAGAGAGTTTGGTGAAAAAGCCAAG                         GTTTGGGATCCGGAGAAGATTGTTGTGATTCCGGATCA
genomic: GTCCTGGTGCTTTTGGTATCTTCAAGAGAGAGTTTGGTGAAAAAGCCAAGgtacgtattc ... cttgctgaagGTTTGGGATCCGGAGAAGATTGTTGTGATTCCGGATCA
EST: gi|125262969|gb|EL277054.1|EL277054
EST:     AGAGAGTTTGGTGAAAAAGCCAAG                         GTTTGGGATCCGGAGAAGATTGTTGTGATTCCGGATCATTATATTTTCACT
genomic: AGAGAGTTTGGTGAAAAAGCCAAGgtacgtattc ... cttgctgaagGTTTGGGATCCGGAGAAGATTGTTGTGATTCCGGATCATTATATTTTCACT
EST: gi|124940533|gb|EL016976.1|EL016976
EST:     AGTTTGGTGAAAAAGCCAAG                         GTTTGGGATCCGGAGAAGATTGTTGTGATTCCGGATCATTATATTTTCACT
genomic: AGTTTGGTGAAAAAGCCAAGgtacgtattc ... cttgctgaagGTTTGGGATCCGGAGAAGATTGTTGTGATTCCGGATCATTATATTTTCACT
EST: gi|124765855|gb|EH855985.1|EH855985
EST:     GTCCTGGTGCTTTTGGTATCTTCAAGAGAGAGTTTGGTGAAAAAGCCAAG                         GTTTGGGATCCGGAGAAGATT
genomic: GTCCTGGTGCTTTTGGTATCTTCAAGAGAGAGTTTGGTGAAAAAGCCAAGgtacgtattc ... cttgctgaagGTTTGGGATCCGGAGAAGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATAACATTTGGGTTAATGTTGATGTTCTTATGACTCATGATGTTTGTGGTCCTGGTGCTTTTGGTATCTTCAAGAGAGAGTTTGGTGAAAAAGCCAAGgtacgtattcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttcttctgtaattatacaaattgagaagagttttgataggtttagtttaggtattagtgaattggtgatcacaatggttgtttagtgtaacttattgtgattgtttacttacttgctgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA