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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTTTAAGAGCAATGGTGCAGGAAACAGTTCAAGGATCTCCTTTGGTTTACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCTgtataacttctctcacttttataaactctttgaattacttggttgttatgtgaatatatgatttgtttagatcttcaattttactctgattttgaaattg...

Basic information

species Arabidopsis thaliana
transcript AT2G42130.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G42130.3 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA02G29260.1 (Glycine max), 5'ss of exon 1
GGTTTTAAGAGCAATGGTGCAGGAAACAGTTCAAGGATCTCCTTTGGTTTACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCTgtataacttctctcacttttataaactctttgaattacttggttgttatgtgaatatatgatttgt-ttagatcttcaattttactctgattttgaaattg-----
||  |  ||||| ||||| ||  || | ||||| ||  | |||   |  || |||| ||||||||| ||||||||||| || |||||||| ||||| |||||  | ||||| |   ||   |  | |         | |||  | || || ||    |  |||||| || |  | |   ||||    |  | ||   |  |     
GGGATGCAGAGCCATGGTTCAACAAGCCGTTCAGGGTGCCCCTGCTGCGTATGCCAAAGAAATGGAACGCCTTTCTGCCAAAGAATCGCTTCTTCTTGCTgtg-agcttcttttctttgcgtgtatttccc-----atttgcgttttctgggacctaaccatttgtctttggccctttgttttgtgtttttgttagtaaagaaacg

upper sequence: AT2G42130.3 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv08s0007g06480.t01 (Vitis vinifera), 5'ss of exon 1
GGTTTTAAGAGCAATGGTGCAGGAAACAGTTCAAGGATCTCCTTTGGTTTACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCTgtataacttct--ctcacttttataaactctttgaattacttggttgttatgtgaatatatgatttgtttagatcttcaattttactctgattttgaaattg-
 ||||  ||||| ||||| ||| |  | |  || ||| ||||       |||||||  ||||||||||| || ||||| |||||||||||||||||||||||  | ||  |   |   || ||     | ||   |  |    |   ||   ||  |  | | ||  ||| ||| || |||  || |    |  ||| |||| 
AGTTTGCAGAGCGATGGTCCAGCAGGCCGCACAGGGAGCTCCGGCAACGTACGCCAAGGAAATGGAGCGGCTCTCTGCCAAGGAATCGCTACTTCTCGCTgtg-agctcataatttgattctaatttttattcacaaaagccagactttcattgttttaaggtttgattttgatttttaatgatattt--gtactgatattga
















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|116394263|gb|EG436855.1|EG436855
EST:     ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCT                         TTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
genomic: ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCTgtataacttc ... ctatgtacagTTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
EST: gi|116394513|gb|EG437105.1|EG437105
EST:     GGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCT                         TTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
genomic: GGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCTgtataacttc ... ctatgtacagTTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
EST: gi|116394262|gb|EG436854.1|EG436854
EST:     ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCT                         TTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
genomic: ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCTgtataacttc ... ctatgtacagTTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
EST: gi|116394258|gb|EG436850.1|EG436850
EST:     ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCT                         TTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
genomic: ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCTgtataacttc ... ctatgtacagTTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
EST: gi|116394668|gb|EG437260.1|EG437260
EST:     ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCT                         TTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
genomic: ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCTgtataacttc ... ctatgtacagTTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
EST: gi|125009746|gb|EL082015.1|EL082015
EST:     ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCT                         TTGAAGGATGCTGGAGGCTTTGAGG
genomic: ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCTgtataacttc ... ctatgtacagTTGAAGGATGCTGGAGGCTTTGAGG
EST: gi|116394267|gb|EG436859.1|EG436859
EST:     ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCT                         TTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
genomic: ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCTgtataacttc ... ctatgtacagTTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
EST: gi|116394271|gb|EG436863.1|EG436863
EST:     ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCT                         TTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
genomic: ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCTgtataacttc ... ctatgtacagTTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
EST: gi|116394264|gb|EG436856.1|EG436856
EST:     ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCT                         TTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
genomic: ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCTgtataacttc ... ctatgtacagTTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
EST: gi|116394268|gb|EG436860.1|EG436860
EST:     ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCT                         TTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT
genomic: ACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCTgtataacttc ... ctatgtacagTTGAAGGATGCTGGAGGCTTTGAGGCTTTAGTTACAGGGAAAACAACTAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTTTAAGAGCAATGGTGCAGGAAACAGTTCAAGGATCTCCTTTGGTTTACGCCAGAGAAATGGAGCGCCTTTCTGCTAAGGAATCGCTACTTCTCGCTgtataacttctctcacttttataaactctttgaattacttggttgttatgtgaatatatgatttgtttagatcttcaattttactctgattttgaaattg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA