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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAACCCAGAGAGGGCAAATGGGCACATCTTCAACGTAGGCAACCCGAACAACGAAGTTACAGTAAGACAGCTCGCTGAAATGATGACCGAGgtgaggaagatggatcagttaggaaactatgaaaatagtttgatttctctgtcgctggttctcaattctcaaaacgaatcatgtttcag

Basic information

species Arabidopsis thaliana
transcript AT2G27860.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 7
GAAAACCCAGAGAGGGCAAATGGGCACATCTTCAACGTAGGCAACCCGAACAACGAAGTTACAGTAAGACAGCTCGCTGAAATGATGACCGAGgtgaggaagatggatcagttaggaaactatgaaaatagt-ttgatttctctgtcgctggttctcaattctcaaaacgaatcatgtttcag
|| || || |  ||||| ||||| ||||||||||| || |||||||| ||||| || ||||| || || ||||| || ||||||||||| |||||||  |||   |||  |||       |   | | |  | || |||| |  | | ||   | |  ||  |          |||  |||||
GATAATCCTGCCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCCAACAATGAGGTTACTGTTAGGCAGCTTGCAGAAATGATGACTGAGgtgaataag--cgattggtttatttgatgcaatattgatctttatttttgggactctatatattgatgtttt---tcttccattcttcag

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 7
GAAAACCCAGAGAGGGCAAATGGGCACATCTTCAACGTAGGCAACCCGAACAACGAAGTTACAGTAAGACAGCTCGCTGAAATGATGACCGAGgtgaggaaga---tggatcagttaggaaactatgaaaatagtttgatttctctgtcgctggttctcaattctcaaaacgaatcatgtttcag
|| || || |  ||||| ||||| ||||||||||| || |||||||| ||||| |||| |||||| |  ||||| || ||||||||||| |||||||   ||    ||| |   ||     | ||| ||  |   |      |||| | | |  |    | |  | |   |    |||  |||||
GATAATCCTGGCAGGGCTAATGGTCACATCTTCAATGTGGGCAACCCAAACAATGAAGCTACAGTTAAGCAGCTTGCAGAAATGATGACTGAGgtgaatgagtcattggtttttttgatgcaatattaatcttaatcttgacctctatggattctatatattgatgacttccttccattattcag

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: PP1S379_19V6.1 (Physcomitrella patens), 5'ss of exon 5
GAAAACCCAGAGAGGGCAAATGGGCACATCTTCAACGTAGGCAACCCGAACAACGAAGTTACAGTAAGACAGCTCGCTGAAATGATGACCGAGgtgagg----aagatggatcagttaggaaacta--tgaaaatagtttgatttctctgtcgct----ggttctcaattctcaaaacga------atcatgtttcag
|||||||| |  || || ||||| |||||||||||||| ||||||||| |||||||||| ||  |     |||| |||||  ||||||| || || ||     |  ||  ||   ||   |    |  | |  | ||| | |    ||||  |       | | ||||  |  ||  |        || |  ||||||
GAAAACCCTGCTAGAGCCAATGGCCACATCTTCAACGTCGGCAACCCGCACAACGAAGTGACCATCCAGGAGCTTGCTGAGCTGATGACTGATgtaagtcaccagaatccattcattttcatttcagctcagcacagtctcacaagtctggtgtgtggaagctatcaaaccctaacccacccttctattaactttcag

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|164156069|gb|ES092989.1|ES092989
EST:     ACCCGAACAACGAAGTTACAGTAAGACAGCTCGCTGAAATGATGACCGAG                         GTTTACGCAAAAGTGAGTGGAGAAGGAGCCA
genomic: ACCCGAACAACGAAGTTACAGTAAGACAGCTCGCTGAAATGATGACCGAGgtgaggaaga ... catgtttcagGTTTACGCAAAAGTGAGTGGAGAAGGAGCCA
EST: gi|116422972|gb|EG465564.1|EG465564
EST:     ACCCGAACAACGAAGTTACAGTAAGACAGCTCGCTGAAATGATGACCGAG                         GTTTACGCAAAAGTGAGTGGAGAAGGAGCCATTGAGAGCCCAACGGTTGAT
genomic: ACCCGAACAACGAAGTTACAGTAAGACAGCTCGCTGAAATGATGACCGAGgtgaggaaga ... catgtttcagGTTTACGCAAAAGTGAGTGGAGAAGGAGCCATTGAGAGCCCAACGGTTGAT
EST: gi|124728519|gb|EH819921.1|EH819921
EST:     ACCCGAACAACGAAGTTACAGTAAGACAGCTCGCTGAAATGATGACCGAG                         GTTTACGCAAAAGTGAGTGG
genomic: ACCCGAACAACGAAGTTACAGTAAGACAGCTCGCTGAAATGATGACCGAGgtgaggaaga ... catgtttcagGTTTACGCAAAAGTGAGTGG
EST: gi|125065657|gb|EL132808.1|EL132808
EST:     CTGAAATGATGACCGAG                         GTTTACGCAAAAGTGAGTGGAGAAGGAGCCATTGAGAGCCCAACGGTTGAT
genomic: CTGAAATGATGACCGAGgtgaggaaga ... catgtttcagGTTTACGCAAAAGTGAGTGGAGAAGGAGCCATTGAGAGCCCAACGGTTGAT
EST: gi|125140091|gb|EL178520.1|EL178520
EST:     ACAGTAAGACAGCTCGCTGAAATGATGACCGAG                         GTTTACGCAAAAGTGAGTGGAGAAGGAGCCATTGAGAGCCCAACGGTTGAT
genomic: ACAGTAAGACAGCTCGCTGAAATGATGACCGAGgtgaggaaga ... catgtttcagGTTTACGCAAAAGTGAGTGGAGAAGGAGCCATTGAGAGCCCAACGGTTGAT
EST: gi|125238062|gb|EL252147.1|EL252147
EST:     ACCCGAACAACGAAGTTACAGTAAGACAGCTCGCTGAAATGATGACCGAG                         GTTTACGCAAAAGTGAGTGGAGAAGGAG
genomic: ACCCGAACAACGAAGTTACAGTAAGACAGCTCGCTGAAATGATGACCGAGgtgaggaaga ... catgtttcagGTTTACGCAAAAGTGAGTGGAGAAGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAACCCAGAGAGGGCAAATGGGCACATCTTCAACGTAGGCAACCCGAACAACGAAGTTACAGTAAGACAGCTCGCTGAAATGATGACCGAGgtgaggaagatggatcagttaggaaactatgaaaatagtttgatttctctgtcgctggttctcaattctcaaaacgaatcatgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC