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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCCAACGGTTGATGTTAGCTCCAAAGAGTTTTACGGGGAAGGTTATGATGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCGgtaattcttcataatcaccaacatgatagataatatgctttaaaatcaaaatcaattgctattctgatagaattttggactttgaaaatag

Basic information

species Arabidopsis thaliana
transcript AT2G27860.1
intron # 8
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 8
lower sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 8
AGCCCAACGGTTGATGTTAGCTCCAAAGAGTTTTACGGGGAAGGTTATGATGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCGgtaattcttcataatcaccaacatgat-agataatatgctttaaaatcaaaatcaattgctattctgatagaattttggactttgaaaatag
|  || ||  ||||||| ||||| ||||| ||||| || || || |||||||||||||||||||||||||| ||||||||||| || |||   || || ||||  | | |  | ||   ||  | |  | ||   |  | |||| ||   ||   | |  | || | | |   |  | |  | |      ||
ACACCTACCATTGATGTGAGCTCAAAAGAATTTTATGGTGAGGGATATGATGACAGTGACAAGAGAATCCCTGACATGACCATAATAAACAAGCAGCTTGgtaggtttactcagtcgttaatttaaccatatttgaccccttaagattgtaacttacttttcttgtta-atggtcattgcttctcctctcag

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA12G30490.1 (Glycine max), 5'ss of exon 8
AGCCCAACGGTTGATGTTAGCTCCAAAGAGTTTTACGGGGAAGGTTATGATGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCGgtaattcttcataatcaccaacatgatagataatatgctttaaaatcaaaatcaattgctattctgatagaa--ttttggac-------tttgaaaatag----------------------------------
|  || ||  ||||||| ||||||||||| ||||| || || || |||||||| |||||||||||||| || ||||||||||| |||||  | || || ||||  | | | |  ||  |   |   | || | |||    |||||| | ||    | |  || |||| | |   ||||| ||       | | ||||||                                   
AAACCTACTATTGATGTGAGCTCCAAAGAATTTTATGGTGAGGGATATGATGATAGTGACAAGAGAATTCCTGACATGACCATAATTAATAGGCAGCTTGgtatgtttccttgttctactctacctttgagattat----taaaatgagaaatgctaggaatactgacacagtcttttgaacaaactcctcttaaaataatttacctgttaatggggtgttacttctttatcag

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA12G08930.1 (Glycine max), 5'ss of exon 8
AGCCCAACGGTTGATGTTAGCTCCAAAGAGTTTTACGGGGAAGGTTATGATGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCGgtaattcttcataatcaccaacatga---tagataatatgctttaaaatcaaaatcaattgctattctgatagaattttggactttgaaaatag
|  || || |||||||| ||||| ||||| ||||| || || || |||||||| ||||||||||||||||| ||||||||||| || ||| | || || ||||  | | |  | ||   ||  | |   ||  | |     || | | |  || | ||||    |  | || |   ||    || | |      
ACACCTACCGTTGATGTGAGCTCAAAAGAATTTTATGGTGAGGGATATGATGATAGTGACAAGAGAATCCCTGACATGACCATAATAAACAGGCAGCTTGgtaggtttcctcactctttaatttaaccatatttgacccttttaagattgtaacttaatttacctgttaatggtcattgcttctctcag-----

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA17G05440.1 (Glycine max), 5'ss of exon 6
AGCCCAACGGTTGATGTTAGCTCCAAAGAGTTTTACGGGGAAGGTTATGATGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCGgtaattcttcataatcaccaacatgatagataatatgctttaaaatcaaaatcaattgctattctgatagaattttggactttgaaaatag
|  || ||  ||||||| || |||||||| ||||| || || || |||||||| |||||||||||||| || ||||||||||| |||||  | || || ||||  | | | |  |     || | |    |||  |   |||||||  ||   || || ||    | ||  | ||      |         
AAACCTACTATTGATGTGAGTTCCAAAGAATTTTATGGTGAGGGATATGATGATAGTGACAAGAGAATTCCTGACATGACCATAATTAATAGGCAGCTTGgtatgtttccttgtttt---actttacctttaa-gtttattaaaat--aatctaactgttaacggggtattacttcttttatcag------

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 8
AGCCCAACGGTTGATGTTAGCTCCAAAGAGTTTTACGGGGAAGGTTATGATGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCGgtaattcttcataatcaccaacatgatagataatatgctttaaaatcaaaatcaattgctattctgatagaa-ttttggactttgaaaatag
   ||||| |||||||| ||||||||||| || || || ||||| ||||||||||||||||||||||| |||||||||||||| || ||    ||||| ||||||  |   |  ||   | |||      |    |  |||    |   | | ||     ||||||| | || |||||||          ||
GTACCAACTGTTGATGTAAGCTCCAAAGAATTCTATGGTGAAGGATATGATGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtaatgatctgttttctttatcattcctcctctgttcttttgcggttggagtgaa-----attctgacacaacttttggatggaattgccag

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 8
AGCCCAACGGTTGATGTTAGCTCCAAAGAGTTTTACGGGGAAGGTTATGATGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCGgtaattcttcataatcaccaacatgatagataatatgctttaaaatcaaaatcaattgctattctgatagaattttggactttgaaaatag
   ||||| || ||||| ||||||||||| || || || || || ||||||||||||||||||||||| |||||||||||||| || ||    ||||| ||||   |    |  || | | |||      |    |  ||| |  |   | | ||     ||||||| | || ||| | |           
GTACCAACTGTGGATGTAAGCTCCAAAGAATTCTATGGTGAGGGATATGATGACAGTGACAAGAGAATTCCAGACATGACCATAATCAATAAACAACTTGgtatcgccctgttttctctatcattcctcctttgttcttttgaggttggagtaaa-----attctgacacaacttttgccag---------

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: EFJ07025 (Selaginella moellendorffii), 5'ss of exon 8
-AGCCCAACGGTTGATGTTAGCTCCAAAGAGTTTTACGGGGAAGGTTATGATGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCGgtaattcttcataatcaccaacatgatagataatatgctttaaaatcaaaatcaattgctattctgatagaattttggactttgaaaatag
 |||||| |  | || || ||||| || |||||||||||||| || || |||||||| |||||| | || ||||||||||| ||||| ||    ||||| |||||    | |  |||       |      |  | |       ||||      ||       |||  |    ||||||  |||||    ||
GAGCCCA-CAATCGACGTGAGCTCGAAGGAGTTTTACGGGGAGGGATACGATGACAGCGACAAGCGCATTCCAGACATGACGATCATCAAGAAGCAACTGGgtaagagct-acgatcgt-gttctagcttttgttctatcaaccaatcgtgtctaaacatctctctc-tctctttttggtgtttgatc-cag

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: EFJ18978 (Selaginella moellendorffii), 5'ss of exon 8
-AGCCCAACGGTTGATGTTAGCTCCAAAGAGTTTTACGGGGAAGGTTATGATGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCGgtaattcttcataatcaccaacatgatagataatatgctttaaaatcaaaatcaattgctattctgatagaattttggactttgaaaatag
 |||||| |  | || || ||||| || |||||||||||||| || ||||||||||| |||||| | || ||||||||||| ||||| ||    ||||| |||||    | |  |||       |      |  | |       ||||      ||       |||  |    ||||||  |||||    ||
GAGCCCA-CAATCGACGTGAGCTCGAAGGAGTTTTACGGGGAGGGATATGATGACAGCGACAAGCGCATTCCAGACATGACGATCATCAAGAAGCAACTGGgtaagagct-acgatcgt-gttctagcttttgttctatcaaccaatcgtgtctaaacatctctctc-tctctttttggtgtttgatc-cag

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|116380182|gb|EG422774.1|EG422774
EST:     TGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCG                         GATGGAACCCGAAAACATCGCTATGGGATTTGCTTGAGTGGACCTTAACCT
genomic: TGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCGgtaattcttc ... ttgaaaatagGATGGAACCCGAAAACATCGCTATGGGACTTGCTCGAGTCGACCTTAACCT
EST: gi|124825938|gb|EH910804.1|EH910804
EST:     TGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCG                         GATGGAACCCGAAAACATCGCTATGGGACTTG
genomic: TGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCGgtaattcttc ... ttgaaaatagGATGGAACCCGAAAACATCGCTATGGGACTTG
EST: gi|116422972|gb|EG465564.1|EG465564
EST:     TGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCG                         GATGGAACCCGAAAACATCGCTA
genomic: TGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCGgtaattcttc ... ttgaaaatagGATGGAACCCGAAAACATCGCTA
EST: gi|125111800|gb|EL163132.1|EL163132
EST:     CAAGAGAATCCCAGACATGACCATTCATTAACCGCCAACTCG                         GATGGAACCCGAAAACATCGCTATGGGACTTGCTCGAGTCGACCTTAACCT
genomic: CAAGAGAATCCCAGACATGACCA-TCATTAACCGCCAACTCGgtaattcttc ... ttgaaaatagGATGGAACCCGAAAACATCGCTATGGGACTTGCTCGAGTCGACCTTAACCT
EST: gi|125228496|gb|EL242581.1|EL242581
EST:     AGACATGACCATCATTAACCGCCAACTCG                         GATGGAAACCCGAAAACATCGCTATGGGACTTGC
genomic: AGACATGACCATCATTAACCGCCAACTCGgtaattcttc ... ttgaaaatagGATGGAA-CCCGAAAACATCGCTATGGGACTTGC
EST: gi|125275064|gb|EL289149.1|EL289149
EST:     TTAACCGCCAACTCG                         GATGGAACCCGAAAACATCGCTATGGGACTTGCTCGAGTCGACCTTAACCT
genomic: TTAACCGCCAACTCGgtaattcttc ... ttgaaaatagGATGGAACCCGAAAACATCGCTATGGGACTTGCTCGAGTCGACCTTAACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCCAACGGTTGATGTTAGCTCCAAAGAGTTTTACGGGGAAGGTTATGATGACAGTGACAAGAGAATCCCAGACATGACCATCATTAACCGCCAACTCGgtaattcttcataatcaccaacatgatagataatatgctttaaaatcaaaatcaattgctattctgatagaattttggactttgaaaatag

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