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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgttttaattgcaaataacgcttatagttcattgggcttgctggttacaccgttgctattttgccagGTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGAGTACGATTACACAATGGACTTTGATCTCGGTAGCTCAAGCACCTAATAT

Basic information

species Arabidopsis thaliana
transcript AT5G61500.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G61500.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G00830.5 (Glycine max), 3'ss of exon 7
----------------------gtatgtgttt-taattgcaaata-----acgcttatagttcattgggcttgc-tggttacaccgttgctattttgccagGTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGAGTACGATTACACAATGGACTTTGATCTCGGTAGCTCAAGCACCTAATAT
                       ||  ||||  ||||  | || |     | |  | |   ||  ||   |    |  | | |   |   |||||    |||||||| ||  | ||| | || || ||||| || || ||||||||||||||||| |||||||| |||||||||||||| |||||||| ||||  | |   
ctagttcatgagtctaagtgcaataactgttcctaataactaacatatatatgtgtgtgtgtctctgatgtgatataatcatat-atacttatttctgtagGTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGAGTATGATTACACGATGGACTTTGATCTTGGTAGCTCCAGCAATTGACTA

upper sequence: AT5G61500.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G36540.1 (Glycine max), 3'ss of exon 8
--------------------------gtatgtgt-tttaattgcaaata-acgcttata-gttcattgggcttgctggttacaccgttgctattttgccagGTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGAGTACGATTACACAATGGACTTTGATCTCGGTAGCTCAAGCACCTAATAT
                            |         |    || ||| |    |||  ||  ||  ||     |  | | |   |   |||||    |||||||| ||  | ||| | || || ||||| || || ||||||||||||||||| ||||| || |||||||||||||| |||||||| |||   | |   
tgacataactgttcctaataactaacacacacacacacacacacacatatatatatatgtgtctatgaggtaatataatcatat-atacttatttctgtagGTACCTATTTTTATTCCTAAAATTTATGGCTTCTGTAATTCCAACAATTGAGTATGATTATACCATGGACTTTGATCTTGGTAGCTCCAGCCATTGACTA

upper sequence: AT5G61500.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S62_116V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------------gtatgtgttttaatt-gcaaataacgcttatagttcat-tgggcttgctggttacaccgttgctatt--ttgccagGTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGAGTACGATTACACAATGGACTTTGATCTCGGTAGCTCAAGCACCTAATAT
                         |  | || ||||   ||  |     ||    |  ||  || ||   |  |   |   |||  | ||  ||  ||| || || ||| | ||| | || ||| | || || || || ||||| ||||||||||||||||| ||||||||||| || ||  |     |    | || |
tttcgcttggaacattgcatagacctgagagtcttaaccagcccactgtactagctgagcaggtgagcagacctgacgcgaggtttttgttgttttgcagATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGAGTACGATTACACGATGGACTTTGAACTTGGGGGTCAGTGATAGTTATCT

upper sequence: AT5G61500.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S62_116V6.2 (Physcomitrella patens), 3'ss of exon 10
------------------------gtatgtgttttaatt-gcaaataacgcttatagttcat-tgggcttgctggttacaccgttgctatt--ttgccagGTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGAGTACGATTACACAATGGACTTTGATCTCGGTAGCTCAAGCACCTAATAT
                         |  | || ||||   ||  |     ||    |  ||  || ||   |  |   |   |||  | ||  ||  ||| || || ||| | ||| | || ||| | || || || || ||||| ||||||||||||||||| ||||||||||| || ||  | |||   |        
tttcgcttggaacattgcatagacctgagagtcttaaccagcccactgtactagctgagcaggtgagcagacctgacgcgaggtttttgttgttttgcagATATCTTTTCATTTTCCTCAAATTCGTCGCGTCCGTGATACCAACTATTGAGTACGATTACACGATGGACTTTGAACTTGG-GGGTCAGTGA--------

upper sequence: AT5G61500.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ26505 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtgttttaattgcaaataacgcttatagttcattgggcttgctggttacaccgttgctatt-ttgc-cagGTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGAGTACGATTACACAATGGACTTTGATCTCGGTAGCTCAAGCACCTAATAT
               | ||  | | ||| |  ||     |  | ||| |||  || || |  ||| |||| ||||||||| || |||||| | ||||||||||| || || |||||||||||||||||||| || || ||||| ||     | ||    ||| |          
---------------gtaaggatctcttttgttttccctgcttggcttgttg-acagtggacattcttgcgcagGTACCTTTTTCTGTTCCTCAAGTTCATGGCGTCGGTCATTCCAACAATTGAGTACGACTATACGATGGAGTTCACGGTTGGAGCGTCATGA---------

upper sequence: AT5G61500.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ14759 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtgttttaattgcaaataacgcttatagttcattgggcttgctggttacaccgttgctatt-ttgc-cagGTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGAGTACGATTACACAATGGACTTTGATCTCGGTAGCTCAAGCACCTAATAT
                           |||  ||     |  | ||| |||  || || |  ||| |||| ||||||||| || |||||| | ||||||||||| || || ||||||||||| |||||||| || || ||||| ||     | ||    ||| |          
--------------------------gtatgatttccctgcttggcttgttg-acagtggacattcttgcgcagGTACCTTTTTCTGTTCCTCAAGTTCATGGCGTCGGTCATTCCAACAATCGAGTACGACTATACGATGGAGTTCACGGTTGGAGCGTCATGA---------

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|86075572|gb|DR371329.1|DR371329
EST:     AAAATCATTGATGTATTAATGTCGCGTGGAGTAGAACCTGAAGTCGACAA                         GTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGA
genomic: AAAATCATTGATGTATTAATGTCGCGTGGAGTAGAACCTGAAGTCGACAAgtatgtgttt ... attttgccagGTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGA
EST: gi|125267731|gb|EL281816.1|EL281816
EST:     ATGTATTAATGTCGCGTGGAGTAGAACCTGAAGTCGACAA                         GTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGA
genomic: ATGTATTAATGTCGCGTGGAGTAGAACCTGAAGTCGACAAgtatgtgttt ... attttgccagGTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGA
EST: gi|116413789|gb|EG456381.1|EG456381
EST:     AAAATCATTGATGTATTAATGTCGCGTGGAGTAGAACCTGAAGTCGACAA                         GCACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCGACAATTGA
genomic: AAAATCATTGATGTATTAATGTCGCGTGGAGTAGAACCTGAAGTCGACAAgtatgtgttt ... attttgccagGTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGA
EST: gi|124799860|gb|EH889539.1|EH889539
EST:     AAAATCATTGATGTATTAATGTCGCGTGGAGTAGAACCTGAAGTCGACAA                         GTACCTCTTCCTGTT
genomic: AAAATCATTGATGTATTAATGTCGCGTGGAGTAGAACCTGAAGTCGACAAgtatgtgttt ... attttgccagGTACCTCTTCCTGTT
EST: gi|163969504|gb|ES135114.1|ES135114
EST:     GTGGAGTAGAACCTGAAGTCGACAA                         GTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATCGA
genomic: GTGGAGTAGAACCTGAAGTCGACAAgtatgtgttt ... attttgccagGTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaataacgcttatagttcattgggcttgctggttacaccgttgctattttgccagGTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGAGTACGATTACACAATGGACTTTGATCTCGGTAGCTCAAGCACCTAATAT
 aaataac  putative branch site (score: 2)
                                           ctatttt  putative PPT
         ttatagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgttttaattgcaaataacgcttatagttcattgggcttgctggttacaccgttgctattttgccagGTACCTCTTCCTGTTCTTGAAGTTCATGGCATCAGTTATTCCAACAATTGAGTACGATTACACAATGGACTTTGATCTCGGTAGCTCAAGCACCTAATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA