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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatgtaaacttgacttgagttatagaaggaaaacagtgctagcacgttattcttttcgaaaggaacttatttgacccacacattgctttttgtgtgcagCTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC

Basic information

species Arabidopsis thaliana
transcript AT1G78900.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 15
--gcatgtaaacttgacttgagttatagaaggaaaacagtgctagcacgttattcttttcgaaaggaacttatttgacccacacattgctttttgtgtgcagCTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC
   |   | || |||  ||   ||       |   ||  | || ||    | |  | ||     || ||  ||||| || | | ||           | |||||||| || |||||||| || ||||||   || || || |||||||||||||| |||||| | |||||||||||| | || || || || ||||| ||
aaactattcaatttgtattttattgatatttgttgacccttcttgctttgtgtaatattattgtggcacc-atttggccta-atatcttcaccaaatttcagCTTGTTGGTAAAGATGCACTGGCAGAATCTGATAAGATTACATTGGAAACAGCCAAGCTACTAAGGGAAGATTACTTGGCACAGAATGCATTTACCCC

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 12
----------------------------------------------------------------------gcatgtaaacttgacttgagttatagaaggaaaacagtgctagcacgttattcttttcgaaaggaacttatttgacccacacattgctttt-tgtgtgcagCTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC
                                                                        ||||    ||| | ||  || |       |  |||   |   | |  | | |||   ||  | |||   ||| |       |  |||   ||||| |||||||| || ||||||||||| ||||||   ||||| || ||| |||| ||||| |||||| |||| ||||||||  | || ||||| || ||||| ||
gtaggatttgctcatcatcttttccatttacttgcacaaaataccatgatgtttgaactttttttccttattatgtggcattggcatgttttgtc------atgcagcattcaaatgaaaatttttatcaatagcactccattgtcttgattgtgacttccgtgtgttcagCTTGTTGGTAAAGATGCGCTGGCAGAATCTGACAAGATTACACTGGAGACAGCAAAGCTACTGAGAGAAGATTATTTGGCACAAAATGCATTTACCCC

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 16
gcatgtaaacttg--acttgagttatagaaggaaaacagtgctagcacgttattcttttcgaaaggaacttatttgacccacacattg--ctttttgtgtgcagCTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC
   |||    |||    |||    | |   |  |    ||    |||  || |||| ||   |   ||||||  ||   ||   ||||  ||| ||   | |||||||| || || |||||  |||| ||||| || || ||||| || ||||| || ||||| ||||| || ||||| ||||||||||| || ||||||||
---tgttgttttgtagtttggaaaaaatttgtcaggatgtatgtgcat-ttgttctattactagtaaacttaactggatcatttattgaccttgtttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACC

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 16
gcatgtaaacttgacttgagttatagaaggaa---aacagtgctagcacgttattcttttcgaaaggaacttatttgacccacacattg--ctttttgtgtgcagCTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC
     |    |||  |||   | | ||   ||      ||       | |   || || |   |   ||||||  ||   ||   ||||  ||| ||   | |||||||| || || |||||  |||| ||||| || || ||||| || ||||| || ||||| ||||| || ||||| ||||||||||| || ||||||||
-----tggtgttgttttgtagtttggacaaaatttgttaggatgtatatgcatttgttctattagtaaacttaactggatcatttattgaccttgtttaatccagCTTGTGGGCAAGGATGCTTTAGCTGAAGGAGATAAGATCACCTTAGAAACTGCAAAGCTTTTGAGAGAGGATTATCTTGCTCAAAATGCCTTTACACC

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|116463760|gb|EG506352.1|EG506352
EST:     AGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTGTCCAG                         CTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACA
genomic: AGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTGTCCAGgtatgtatca ... ttgtgtgcagCTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACA
EST: gi|125245220|gb|EL259305.1|EL259305
EST:     TCTTAATGAAATTGTCCAG                         CTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACA
genomic: TCTTAATGAAATTGTCCAGgtatgtatca ... ttgtgtgcagCTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACA
EST: gi|116463788|gb|EG506380.1|EG506380
EST:     AGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTGTCCAG                         CTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACA
genomic: AGGCCAGAGAGGTGTTGCAGAGGGAAGACGATCTTAATGAAATTGTCCAGgtatgtatca ... ttgtgtgcagCTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACA
EST: gi|116424281|gb|EG466873.1|EG466873
EST:     TCTTAATGAAATTGTCCAG                         CTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACA
genomic: TCTTAATGAAATTGTCCAGgtatgtatca ... ttgtgtgcagCTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttattcttttcgaaaggaacttatttgacccacacattgctttttgtgtgcagCTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC
                        atttgac  putative branch site (score: 4)
                                      ttgcttttt  putative PPT
                   aacttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgtaaacttgacttgagttatagaaggaaaacagtgctagcacgttattcttttcgaaaggaacttatttgacccacacattgctttttgtgtgcagCTTGTAGGAAAAGATGCGCTAGCAGAAGGGGACAAAATCACATTGGAAACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA