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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctaatcaattgtgctggtggttgagtgacataattcattacttgtttagttgttgactcctacttatattttcagGTACAAGACCTTCTTGCTCAGTGTGGCGAGCATCTTGAGAAAGGTGACATCCACCAGGGTCCAGCTGTGCTTGGGTTAGCAATGGTTGCTATGTCTGAAG

Basic information

species Arabidopsis thaliana
transcript AT2G20580.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 18
gtatctaatcaattgtgct----ggtggttg-agtgacataattcattacttgtttagttgttgactcctacttatatttt---cagGTACAAGACCTTCTTGCTCAGTGTGGCGAGCATCTTGAGAAAGGTGACATCCACCAGGGTCCAGCTGTGCTTGGGTTAGCAATGGTTGCTATGTCTGAAG
|||  | ||   |  ||||    |||  |||  |   ||   ||  |||  | |  || | ||||           |||||   ||||| ||| | || ||||     ||     ||||||||||||||||||| | ||||||||| |||||||| || ||  | ||  |  |||| ||| ||||||
gtacttcatgtttaatgcttagaggttcttgtggcttcaagcttgtttaaatttcgaggttttgatatgcttggcaattttacgcagGTTCAAAAGCTCCTTGGGATTTGCTCACAGCATCTTGAGAAAGGTGAAACCCACCAGGGGCCAGCTGTCCTAGGAATTGCGCTTATTGCAATGGCTGAAG

upper sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA12G13410.1 (Glycine max), 3'ss of exon 18
-----------------------------------------------gtatctaatcaat-----tgtgctggtggttgagtgacataattcattacttgtttagttgttgactcctacttatattttcagGTACAAGACCTTCTTGCTCAGTGTGGCGAGCATCTTGAGAAAGGTGACATCCACCAGGGTCCAGCTGTGCTTGGGTTAGCAATGGTTGCTATGTCTGAAG
                                                 ||||  |  |      | || |  |  |||  |||   | ||  | | || | || ||| |||  | |  ||    || ||||| ||| | ||  | | ||| |||    | |||||||| |||||||| |  ||||||||||| |||||||||||  | || ||||| |||||| ||||||
gtacaatcttgtgatgaattagttatgaagttttttttaaaaatgtaacatctgctacacctttctatgtttataattgc-tgatgcattttttcatttttgtatttgctgatgcttcttt---cttgcagGTTCAAAATCTGTTGGGTCATTGTTCACAACATCTTGATAAAGGTGAAACTCACCAGGGTCCTGCTGTGCTTGGAATTGCTATGGTAGCTATGGCTGAAG
















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|86050680|gb|DR346435.1|DR346435
EST:     ATATGACACTTCTTTCTTGTGCTTATGCTGGAACTGGAAATGTCCTAAAG                         GTACAAGACCTTCTTGCTCAGTGTGGCGAGCATCTTGAGAAAGGTGACATC
genomic: ATATGACACTTCTTTCTTGTGCTTATGCTGGAACTGGAAATGTCCTAAAGgtatctaatc ... atattttcagGTACAAGACCTTCTTGCTCAGTGTGGCGAGCATCTTGAGAAAGGTGACATC
EST: gi|125209769|gb|EL224723.1|EL224723
EST:     ACTTCTTTCTTGTGCTTATGCTGGAACTGGAAATGTCCTAAAG                         GTACAAGACCTTCTTGCTCAGTGTGGCGAGCATCTTGAGAAAGGTGACATC
genomic: ACTTCTTTCTTGTGCTTATGCTGGAACTGGAAATGTCCTAAAGgtatctaatc ... atattttcagGTACAAGACCTTCTTGCTCAGTGTGGCGAGCATCTTGAGAAAGGTGACATC
EST: gi|116456407|gb|EG498999.1|EG498999
EST:     ATATGACACTTCTTTCTTGTGCTTATGCTGGAACTGGAAATGTCCTAAAG                         GTACAAGACCTTCTTGCTCAGTGTGGCGAGCATCTTGAGAAAGGTGACATC
genomic: ATATGACACTTCTTTCTTGTGCTTATGCTGGAACTGGAAATGTCCTAAAGgtatctaatc ... atattttcagGTACAAGACCTTCTTGCTCAGTGTGGCGAGCATCTTGAGAAAGGTGACATC
EST: gi|124869180|gb|EH953617.1|EH953617
EST:     ATATGACACTTCTTTCTTGTGCTTATGCTGGAACTGGAAATGTCCTAAAG                         GTACAAGACCTTCTTG
genomic: ATATGACACTTCTTTCTTGTGCTTATGCTGGAACTGGAAATGTCCTAAAGgtatctaatc ... atattttcagGTACAAGACCTTCTTG
EST: gi|86050681|gb|DR346436.1|DR346436
EST:     ATATGACACTTCTTTCTTCTGCTTATGCTGGAACTGGAAATGTCCTAAAG                         GTACAAGACCTTCTTGCTCAGTGTGGCGAGCATCTTGAGAAAGGTGACATC
genomic: ATATGACACTTCTTTCTTGTGCTTATGCTGGAACTGGAAATGTCCTAAAGgtatctaatc ... atattttcagGTACAAGACCTTCTTGCTCAGTGTGGCGAGCATCTTGAGAAAGGTGACATC
EST: gi|86050682|gb|DR346437.1|DR346437
EST:     ATATGACACTTCTTTCTTGTGCTTATGCTGGAACTGGAAATGTCCTAAAG                         GTACAAGACCTTCTTGCTCAGTGTGGCGAGCATCTTGAGAAAGGTGACATC
genomic: ATATGACACTTCTTTCTTGTGCTTATGCTGGAACTGGAAATGTCCTAAAGgtatctaatc ... atattttcagGTACAAGACCTTCTTGCTCAGTGTGGCGAGCATCTTGAGAAAGGTGACATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgagtgacataattcattacttgtttagttgttgactcctacttatattttcagGTACAAGACCTTCTTGCTCAGTGTGGCGAGCATCTTGAGAAAGGTGACATCCACCAGGGTCCAGCTGTGCTTGGGTTAGCAATGGTTGCTATGTCTGAAG
                              tgttgac  putative branch site (score: 3)
                                              tattttc  putative PPT
         ataattcattactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctaatcaattgtgctggtggttgagtgacataattcattacttgtttagttgttgactcctacttatattttcagGTACAAGACCTTCTTGCTCAGTGTGGCGAGCATCTTGAGAAAGGTGACATCCACCAGGGTCCAGCTGTGCTTGGGTTAGCAATGGTTGCTATGTCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG