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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTCCAGACCGAGTATTTATGAAACTCATTGTCTGTGCAAACACCAATAAAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCAGgtttcattttttaacatgattggtattctctgaaaagtaatcacggaaaacatatatgattgaatatgaattttattttacaatttttcag

Basic information

species Arabidopsis thaliana
transcript AT3G54660.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G54660.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA02G16010.2 (Glycine max), 5'ss of exon 8
ACTTCCAGACCGAGTATTTATGAAACTCATTGTCTGTGCAAACACCAATAAAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCAGgtttc----attttttaacatgattggtattctctgaaaagtaatcacggaaaacatatatgattgaatatgaattttattttacaatttttcag
 ||||||||||| || ||||||||| |  | ||||||||||| || ||| ||||||| ||| | || ||||||||||||||| | || |||||  | |||||||      |||||  |  || |   |||| | |  | | | ||    ||      |  | | |  ||||  ||||   || | |      |||
GCTTCCAGACCGGGTTTTTATGAAATTAGTAGTCTGTGCAAAAACAAATGAAGTTCTAGGTTTGCATATGTGTGGAGAAGATGCTCCTGAAATTGTGCAGgtttttagagtttttacagctgctctatattgttttgataatgatacatgagttttcaattcacttgatatacattt-gcttgata----cccag

upper sequence: AT3G54660.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv07s0141g00390.t01 (Vitis vinifera), 5'ss of exon 8
ACTTCCAGACCGAGTATTTATGAAACTCATTGTCTGTGCAAACACCAATAAAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCAGgtttcattttttaacatgattggtattctctgaaaagtaatcacggaaaacatatatgattgaatatgaattttattttacaatttttcag
||| |||||||| || || |||||||| || ||||||||||| || || ||||| || ||  | || ||||||||||||||||||||||||||  | |||||||   || | | |         |||   |||    |  |      |     |  | ||||  | |    ||  | |  |||     |||
ACTCCCAGACCGGGTTTTCATGAAACTTATAGTCTGTGCAAAGACTAACAAAGTACTGGGATTGCATATGTGTGGAGAAGATTCACCAGAAATTGTGCAGgtttgccttctaatc--------cattgcttgacttatttttgttagatctgcaattaattggttgta---ttcttatggcaaaaccccag
















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|86061673|gb|DR357430.1|DR357430
EST:     AAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCGG                         GGAKTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT
genomic: AAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCAGgtttcatttt ... aatttttcagGGATTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT
EST: gi|116472768|gb|EG515360.1|EG515360
EST:     AAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCAG                         GGATTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT
genomic: AAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCAGgtttcatttt ... aatttttcagGGATTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT
EST: gi|86061670|gb|DR357427.1|DR357427
EST:     AAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCGG                         GGATTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT
genomic: AAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCAGgtttcatttt ... aatttttcagGGATTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT
EST: gi|86061672|gb|DR357429.1|DR357429
EST:     AAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCGG                         GGATTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT
genomic: AAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCAGgtttcatttt ... aatttttcagGGATTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT
EST: gi|86061674|gb|DR357431.1|DR357431
EST:     AAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCGG                         GGATTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT
genomic: AAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCAGgtttcatttt ... aatttttcagGGATTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT
EST: gi|86061671|gb|DR357428.1|DR357428
EST:     AAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCGG                         GGATTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT
genomic: AAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCAGgtttcatttt ... aatttttcagGGATTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT
EST: gi|86078733|gb|DR374490.1|DR374490
EST:     AAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCGG                         GGATTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT
genomic: AAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCAGgtttcatttt ... aatttttcagGGATTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT
EST: gi|86086942|gb|DR382701.1|DR382701
EST:     AAGTTYTCGGTGTTCACATGTGTGGAGAAGATTCMCCAGAAATCATCCGG                         GGATTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT
genomic: AAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCAGgtttcatttt ... aatttttcagGGATTTGGGGTTGCAGTTAAAGCTGGTTTAACTAAGGCCGACTTTGATGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTCCAGACCGAGTATTTATGAAACTCATTGTCTGTGCAAACACCAATAAAGTTCTCGGTGTTCACATGTGTGGAGAAGATTCACCAGAAATCATCCAGgtttcattttttaacatgattggtattctctgaaaagtaatcacggaaaacatatatgattgaatatgaattttattttacaatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA