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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgaaggcgtagaactacaattttcatattgtcaattcttgctaccttttgttatgtaattttgtgatgttttcctttagtttgaagtattgccactgaagtttgaagtattttctcttagTGTTTGTTTGCAACAGAGACATTTAGTATTGGATTGAACATGCCGGCAAAGACGGTTGTATTTACCAATGTACGTAAGTTTGATGGAGACAAGTTCCGGT

Basic information

species Arabidopsis thaliana
transcript AT1G59760.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G59760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g18140.1 (Oryza sativa), 3'ss of exon 6
gtaggtgaaggcgtagaactacaattttcatattgtcaattcttgctaccttttgttatgtaattttgtgatgttttcctttagtttg-aagtattgccactgaagtttgaagtattttctcttagTGTTTGTTTGCAACAGAGACATTTAGTATTGGATTGAACATGCCGGCAAAGACGGTTGTATTTACCAATGTACGTAAGTTTGATGGAGACAAGTTCCGGT
                          || ||  | |  |   | ||   ||| | |    ||  | | | |  | | |||||   ||| || | ||  |     || |||||   || | |  ||||| |||||||| ||||| ||||| |||||||| ||||||||||| |||||||| ||||| ||||||||||| || || ||||| || ||    ||| | |
--------------------------tttattatatggagcttagcacacttgtatgccttatctatttaagatatacctttttgttgtaacttttagcttctgagattgaaaccttgtgttgtagTGCTTGTTTGCCACAGAAACATTCAGTATTGGTTTGAACATGCCTGCAAAGACTGTTGTGTTTACCAATGTGCGAAAATTTGACGGTGATCGATTCAGAT

upper sequence: AT1G59760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G040995_T02 (Zea mays), 3'ss of exon 6
gtaggtgaaggcgtagaactacaattttcatattgtcaattcttgctaccttttgttatgtaattttgtgatgttttcctttagtttgaagtattgccactgaagtttgaagtattttctcttagTGTTTGTTTGCAACAGAGACATTTAGTATTGGATTGAACATGCCGGCAAAGACGGTTGTATTTACCAATGTACGTAAGTTTGATGGAGACAAGTTCCGGT
                   | || |   ||| ||    ||  || ||  || |    |    ||  |||| || | | | ||  | |      ||    ||||| ||  ||  ||  | |  |||||||||||||| ||||| ||||| |||||||| ||||||||||| |||||||| ||||| ||||||||||| || || ||||| ||||||   ||| | |
-----------------cttccactgagcattttagatatgttttctttctatctcaagactatgctgtg-tgctgtacctttttat------ttcttgctgaaatt-aaaacatggtgttatagTGTTTGTTTGCCACAGAAACATTCAGTATTGGTTTGAACATGCCTGCAAAGACTGTTGTGTTTACCAATGTGCGAAAATTTGACGGAGACCGATTCAGAT

upper sequence: AT1G59760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G47700.1 (Glycine max), 3'ss of exon 6
gtaggtgaaggcgtagaactacaattttcatattgtcaattcttgctaccttttgttatgtaattttgtgatgttttcctttagtttgaagtattgccactgaagtttgaagtattttctcttagTGTTTGTTTGCAACAGAGACATTTAGTATTGGATTGAACATGCCGGCAAAGACGGTTGTATTTACCAATGTACGTAAGTTTGATGGAGACAAGTTCCGGT
             | || ||    | || ||||||  |    |    | | ||  ||   |||  || | |    ||| | |  ||  || || ||             || ||||||    |||||||||||||| || ||||||||||| ||||| ||||||||||| ||||| || ||||| || || ||||| || |||||||| || ||||||||  |||
---------tcatttgatcttttgtcttaatattgatacagttaagaatccttgtttgattaaaattattaa---ttcttgtgattctaactactg-------------aaatatttttctgtagTGTTTGTTTGCCACCGAGACATTTAGCATTGGTTTGAACATGCCTGCAAAAACTGTTGTTTTCACAAATGTCCGGAAGTTTGACGGGGACAAGTTTAGGT

upper sequence: AT1G59760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv06s0009g01750.t01 (Vitis vinifera), 3'ss of exon 6
gtaggtgaaggcgtagaactacaattttcatattgtca-attcttgctaccttttgtt--atg-taattttgtgatgttttcctttagtttgaagtattgccactgaagtttgaagtattttctcttagTGTTTGTTTGCAACAGAGACATTTAGTATTGGATTGAACATGCCGGCAAAGACGGTTGTATTTACCAATGTACGTAAGTTTGATGGAGACAAGTTCCGGT
                             | |||   | ||||| |  ||| |||||   ||| | | |   || |  ||   |  | |||  ||   |||   | ||  ||||| | |||||  ||||||||||||||| |||||||| || || ||||| ||||||||||| |||||||| || || ||||| ||||| ||||| |||||||| || || ||  | |
----------------------------aaaattagaatattctagtcaccgtttgtccaatggtgaatccttgctaattaattaaattttttaggtgtgct-ttaaatattgaaatgttttcctttagTGTTTGTTTGCCACAGAGACTTTCAGCATTGGTTTGAACATGCCAGCAAAGACTGTAGTGTTTACAAATGTTCGTAAATTTGATGGGGATAAATTTAGAT

upper sequence: AT1G59760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S69_14V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaggtgaaggcgtagaactacaattttcatattgtcaattcttgctaccttttgtt-atgtaattttgtgatgttttcctttagtttgaagtattgccactgaagtttgaagtattttctcttagTGTTTGTTTGCAACAGAGACATTTAGTATTGGATTGAACATGCCGGCAAAGACGGTTGTATTTACCAATGTACGTAAGTTTGATGGAGACAAGTTCCGGT
           ||   || ||   || | ||| |    ||    | | | ||   || | |||| |  || | |        | ||    |  |||| |  ||  ||  |              |||| || ||||||||||| ||||| ||||| || ||||||||||| || || || |||||||||||||| || |||||||||||||| ||||| || || |
-----------cgagaaaataagtttgtgatactactgatgtgagttgcattcaattcaggtaagt--gttaggaaaggagctggtggataacattgtctttgtggtggg-------------cagTGCTTATTTGCAACAGAAACATTCAGTATAGGCTTGAACATGCCAGCCAAAACTGTTGTATTTACCAACGTTCGTAAGTTTGATGGGGACAAATTTCGAT

upper sequence: AT1G59760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ21372 (Selaginella moellendorffii), 3'ss of exon 6
gtaggtgaaggcgtagaactacaattttcatattgtcaattcttgctaccttttgttatgtaattttgtgatgttttcctttagtttgaagtattgccactgaagtttgaagtattttctcttagTGTTTGTTTGCAACAGAGACATTTAGTATTGGATTGAACATGCCGGCAAAGACGGTTGTATTTACCAATGTACGTAAGTTTGATGGAGACAAGTTCCGGT
                                                                       | | ||  |  ||  |   || |   | || |  | |    | ||       ||||  ||||||| ||||||||||| ||||||||| |||| ||||| || ||||| || || || || || || || ||||||||||| |||||||| || |
----------------------------------------------------------------------gtatatttgtgcagcgtttcgtttcttc-ctaagttgttggatgttgc-----agTGCCTGTTTGCTACAGAGACATTCAGTATTGGACTGAATATGCCTGCCAAGACAGTCGTGTTCACGAACGTTCGCAAGTTTGATGGTGACAAGTTTCGCT

upper sequence: AT1G59760.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ23732 (Selaginella moellendorffii), 3'ss of exon 6
gtaggtgaaggcgtagaactacaattttcatattgtcaattcttgctaccttttgttatgtaattttgtgatgttttcctttagtttgaagtattgccactgaagtttgaagtattttctcttagTGTTTGTTTGCAACAGAGACATTTAGTATTGGATTGAACATGCCGGCAAAGACGGTTGTATTTACCAATGTACGTAAGTTTGATGGAGACAAGTTCCGGT
                                                                       | | ||  |  ||  |   || |   | || |  | |    | ||       ||||  ||||||| ||||||||||| ||||||||| |||| ||||| || ||||| || || || || || || || ||||||||||| |||||||| || |
----------------------------------------------------------------------gtatatttgtacagcgtttcgtttcttc-ctaagttgttggatgttgc-----agTGCCTGTTTGCTACAGAGACATTCAGTATTGGACTGAATATGCCTGCCAAGACAGTCGTGTTCACGAACGTTCGCAAGTTTGATGGTGACAAGTTTCGCT

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|164077832|gb|ES161208.1|ES161208
EST:     ATTATTTCAGGAAGGTCTTATTAAG                         TGTTTGTTTGCAACAGAGACATTTAGTATTGGATTGAACAATGCCGGCAAA
genomic: ATTATTTCAGGAAGGTCTTATTAAGgtaggtgaag ... tttctcttagTGTTTGTTTGCAACAGAGACATTTAGTATTGGATTGAACA-TGCCGGCAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttttcctttagtttgaagtattgccactgaagtttgaagtattttctcttagTGTTTGTTTGCAACAGAGACATTTAGTATTGGATTGAACATGCCGGCAAAGACGGTTGTATTTACCAATGTACGTAAGTTTGATGGAGACAAGTTCCGGT
                                          tattttctctt  CT-rich tract
                                       aagtatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtgaaggcgtagaactacaattttcatattgtcaattcttgctaccttttgttatgtaattttgtgatgttttcctttagtttgaagtattgccactgaagtttgaagtattttctcttagTGTTTGTTTGCAACAGAGACATTTAGTATTGGATTGAACATGCCGGCAAAGACGGTTGTATTTACCAATGTACGTAAGTTTGATGGAGACAAGTTCCGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA