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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggttttgctcttgaacagagtatttaagatggtcattttatcttcattcctctcacggttgttgtattgttctgtag

Basic information

species Arabidopsis thaliana
transcript AT1G56340.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 7
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggttttgctcttga-acaga-gtatttaagatggtcattttatcttcattcctctcacggttgttgtattgttctgtag
|||||||||||||||||||| |||||||||||||||||||| || |||||||| ||||| |||||||| ||   ||||||||  ||||| ||    | |   |  |||  |||| | | || | |   |    |  |  |  || ||  ||      | || |  || |  ||
CCTGAGGACTGGGATGATGAGGAAGATGGTGAGTGGACTGCACCAACCATTCCTAACCCTGAGTACAAGGGACCATGGAAGCAAAAGgtgtgaatatctgtttactgatgcagatgcacttgaaacacttgcatatttctggtttctgacataaacat-gtttctttttccag

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os03g61670.1 (Oryza sativa), 5'ss of exon 7
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggttttgctcttgaacagagtatttaagatggtcattttatcttcattcctctcacggttgttgtattgttctgtag----------------
|||||||||||||||||||| |||||||| || ||||| || || |||||||| ||||| |||||||| ||   |||||| |  ||||| ||   || |  ||   ||| ||   |||||   | | ||   ||  ||||      ||||| ||  |   |  ||   |                  
CCTGAGGACTGGGATGATGAGGAAGATGGAGAATGGACAGCTCCAACCATTCCAAACCCTGAGTACAAGGGACCATGGAACCAAAAGgtatg--agtgtgact---gaatagttcatttactctagacaagctaggttcagca---tcacgattactcactaattgcatgaaattttgtgtgtttag

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 7
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggttttgctcttgaacagagtatttaagatggtcattttatcttcattcctctcacggt-tgttgtattgttctgtag
||||||||||||||||| || ||||||||||| |||||||||||||||||||||||||| || ||||| ||   |||||| |  ||||| ||   |||     ||||||| |  ||   |      ||| || || |||     ||| || |  ||||  | |   | |   
CCTGAGGACTGGGATGACGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAAGGACCATGGAAACAAAAGgtatggcagttc----cttgaactgtatacaaactgacatcaattcatattctgatatctgacagcatgtttcacttgccag---

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G358059_T01 (Zea mays), 5'ss of exon 7
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggttttgctcttgaacagagtatttaagatggtcattttatcttcattcctctcacggt-tgttgtattgttctgtag
|||||||||||||| ||||| ||||||||||| |||||||||||||||||||||||||| || ||||| ||   |||||| |  ||||| ||   |||   || || | |     | |   ||  | || || || |||     ||| || |  |||||| |   |    ||
CCTGAGGACTGGGACGATGAGGAAGATGGTGAATGGACTGCCCCTACCATTCCCAACCCAGAATACAAGGGACCATGGAAACAAAAGgtatggcagttc--cttttaacctataaact---gacag-caattcatattctgatatctgacagcatgttgtttcacttgccag

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA10G28890.1 (Glycine max), 5'ss of exon 7
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggttttgctcttgaa----cagagtatttaagatg-gtcattttatcttcattcctctcacgg--ttgttgtattgttctgtag---------------
||||| || ||||||||||| |||||||||||||||||  ||||||||||| ||||||| |||||||| ||   ||||||| |  |||||||| |   ||  | ||| |       | ||||| | ||  | ||| ||   ||   |    | | |   ||| | | |   | || |                
CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGAGTACAAGGGCCCATGGAAGGCAGAGgtttgtggaaatttttattgtaaatttgtaatatttgaaatacgacatattccattatgtttggtaatgaatttgctttctaactttgcatgctacatatttgcag

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 7
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggttttgctcttgaa----cagagtatttaagatg-gtcattttatcttcattcctctcacgg--ttgttgtattgttctgtag---------------
||||| || ||||||||||| |||||||||||||||||  ||||||||||| ||||||| || ||||| ||   ||||||| | ||||||||| |   ||  | ||| |       | ||| | | ||  | ||| ||  | | ||   |   | |   ||| | |||   | || |                
CCTGAAGATTGGGATGATGAGGAAGATGGTGAGTGGACACCCCCTACCATTGCCAACCCTGATTACAAGGGCCCATGGAAGGCAAAGgtttgtggaaatttgttttgtaaatttgtaatatatgaaatatgacatatt-ccattatgtttggaatgaatttgctttataactttgcatgctacatatttgcag

upper sequence: AT1G56340.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 7
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgt----tggttttgctcttgaacagagtatttaagatggtcattttatcttcattcctctcacggttgttgtattgttctgtag
||||| || ||||||||||| ||||||||||| ||||| || || |||||| |||||||||||||||| ||   ||||||||| |||||||||    |||||||  | |       |  ||||||  | |    |  |     | |  ||  |       | |||   |  | ||
CCTGAAGATTGGGATGATGAGGAAGATGGTGAATGGACAGCTCCAACCATTGCCAACCCCGAGTACAAGGGACCATGGAAGCCAAAGgtttgtggcatggttttagtttaagttgaaacatttaattttgctggtaaaa---gagttgtcataattcctctctatctcttggcag

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|86064682|gb|DR360439.1|DR360439
EST:     CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG                         AAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATGATCGAC
genomic: CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggt ... tgttctgtagAAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATGATCGAC
EST: gi|124835539|gb|EH919978.1|EH919978
EST:     CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG                         AAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAA
genomic: CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggt ... tgttctgtagAAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAA
EST: gi|116465699|gb|EG508291.1|EG508291
EST:     CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG                         AAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATGATCGAC
genomic: CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggt ... tgttctgtagAAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATGATCGAC
EST: gi|116471772|gb|EG514364.1|EG514364
EST:     CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG                         AAAATTAAGAACCCCGCTTACA
genomic: CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggt ... tgttctgtagAAAATTAAGAACCCCGCTTACA
EST: gi|116465718|gb|EG508310.1|EG508310
EST:     CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG                         AAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATGATCGAC
genomic: CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggt ... tgttctgtagAAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATGATCGAC
EST: gi|116465735|gb|EG508327.1|EG508327
EST:     CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG                         AAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATGATCGAC
genomic: CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggt ... tgttctgtagAAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATGATCGAC
EST: gi|125241870|gb|EL255955.1|EL255955
EST:     TACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG                         AAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATGATCGAC
genomic: TACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggt ... tgttctgtagAAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATGATCGAC
EST: gi|116482410|gb|EG525002.1|EG525002
EST:     CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG                         AAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATGATCGAC
genomic: CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggt ... tgttctgtagAAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATGATCGAC
EST: gi|164013391|gb|ES176434.1|ES176434
EST:     CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAG                         AAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATG
genomic: CTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggt ... tgttctgtagAAAATTAAGAACCCCGCTTACAAGGGCAAGTGGAAGGCTCCAATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGAGGACTGGGATGATGAAGAAGATGGTGAGTGGACTGCCCCTACCATTCCCAACCCCGAGTACAATGGTGAATGGAAGCCCAAGgtttgttggttttgctcttgaacagagtatttaagatggtcattttatcttcattcctctcacggttgttgtattgttctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG