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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatgagtctctcaacaacttacctttgacagaccaagtactcgaacaaaaccgattttgatcagattagttgtttccggtaatgtgcagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAGACTTACATGACTCGCTCTTTCAAGGACTTGAAAGAGATGTGCAAAACTC

Basic information

species Arabidopsis thaliana
transcript AT5G18170.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os03g58040.3 (Oryza sativa), 3'ss of exon 9
----gtatgtatg-agtctctcaac----aacttacctttgacagaccaagtactcgaacaaaacc-gattttgatcagattagttgtttccggtaatgtg-------cagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAGACTTACATGACTCGCTCTTTCAAGGACTTGAAAGAGATGTGCAAAACTC
    ||   |    | |||| |       || | |   |  | |    ||| | ||     || |  ||   ||||      || || | | | |  ||||       ||||||||||| || || |||||||| || |||||||||||| ||||||| ||||| |||||||| ||    |||| |||  |||| ||||||||||  |  |
gtaagttactgcacaatctccctgtgctaaattcagagtaaaaatgtaaagcagtcaggttaagcaagagactgatgcatgaagctgctgctgttcttgtggtttgttcagAACATTCAGGGTTTCATGTGGGACGAGGAGAAGGTGAACAATGAGCTGAAGACCTACATGACCCGTGGGTTCAGGGATGTGAAGGAGATGTGCAGGAGCC

upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 8
gtatgtatgagtctctcaacaactt---acctttgacagaccaagtactcgaacaaaaccgattttgatcagat--tagttgtttccg-gtaatgtgcagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAGACTTACATGACTCGCTCTTTCAAGGACTTGAAAGAGATGTGCAAAACTC
  |  |  | |  ||  ||    ||   |  | ||  |  |||  |  |  ||| |     |   | || | ||  |  || |      ||||    |||||||||||||| || |||||||| || |||||||||||| | ||||||||||| |||||||||      ||||| ||  |||| |||||||||||||| |
tcactttagtggttccaaattcttttacatatatgttaatccacttcatgtaaccattataaggataattaaatgatgattataattatgtaacacacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACTAAAGGGTTCAAAGATGTGAAGGAGATGTGCAAAACCC

upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 9
-------gtatgtatgagtctctcaacaacttacctttgacagaccaagtactcgaacaaaaccgattttgatcagattagttgtttccggtaatgtgcagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAGACTTACATGACTCGCTCTTTCAAGGACTTGAAAGAGATGTGCAAAACTC
       ||   |   | |   |  |||  |    ||      ||| | | |  | | |  |   |  || || | || |    | |   ||||||  |||||||||||||| || |||||||| || |||||||||||| | ||||||||||| ||||||||       ||||| ||  |||| || ||||||||||| |
tacttgagtggttcgaaattcatttacatttacaattatgttaacccacttcatgta-atcattaaggttaattaaatgatgattattatgtaatgcacagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACAACGAGCTAAAGACATACATGACCAAAGGGTTCAAAGATGTGAAGGAAATGTGCAAAACCC

upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 9
gtatgtatgagtctctcaacaact-tacctttgacagaccaagtactcgaacaa---aaccgattttgatcagat-tagttgtt--tccggtaatgtgcagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAGACTTACATGACTCGCTCTTTCAAGGACTTGAAAGAGATGTGCAAAACTC
  |  |     | |   |  || |  | | ||     || || || |  |  ||   | || || | |  |  |  | |||| |  |   || |    |||||||| ||||| || |||||||| || ||||| |||||| ||||||||||||| ||||||||      |||||| ||  |||| || ||||||||||| |
-aaattgctcattttagaggaattgcatccttattgtacaaattaattaattaatataccctatgtagcccttacatggttggtgattttgtgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAGACCTACATGACCAAAGGTTTCAAAGATGTGAAGGAAATGTGCAAAACCC

upper sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G28770.1 (Glycine max), 3'ss of exon 8
gtatgtatgagtctctcaacaact-tacctttg----acagaccaagtactcgaacaaaaccgattttgatcagat-tagttgtt--tccggtaatgtgcagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAGACTTACATGACTCGCTCTTTCAAGGACTTGAAAGAGATGTGCAAAACTC
  |  |     | |   |  || |  |||  ||    ||||   || || |  || | |  | || | |  |  |  | |||| |  |   ||      |||||||| ||||| || |||||||| || ||||| |||||| ||||||||||||| ||||||||      |||||| ||  |||| || ||||||||||| |
-aaattgctcattttagaggaattgcacccctgctgtacaggttaattaatt-aatatactccatgtagtccttacatggttggtgattttgtggcacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAGACCTACATGACCAAAGGTTTCAAAGATGTGAAGGAAATGTGCAAAACCC

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|116445683|gb|EG488275.1|EG488275
EST:     TATATGCAAACTCTGGAGGAGTCACTGTAAGTTACTTCGAATGGGTTCAG                         AACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAG
genomic: TATATGCAAACTCTGGAGGAGTCACTGTAAGTTACTTCGAATGGGTTCAGgtatgtatga ... taatgtgcagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAG
EST: gi|86055070|gb|DR350827.1|DR350827
EST:     TATATGCAAACTCTGGAGGAGTCACTGTAAGTTACTTCGAATGGGTTCAG                         AACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAG
genomic: TATATGCAAACTCTGGAGGAGTCACTGTAAGTTACTTCGAATGGGTTCAGgtatgtatga ... taatgtgcagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAG
EST: gi|116428925|gb|EG471517.1|EG471517
EST:     TATATGCAAACTCTGGAGGAGTCACTGTAAGTTACTTCGAATGGGTTCAG                         AACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAG
genomic: TATATGCAAACTCTGGAGGAGTCACTGTAAGTTACTTCGAATGGGTTCAGgtatgtatga ... taatgtgcagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAG
EST: gi|124953856|gb|EL029002.1|EL029002
EST:     AGGAGTCACTGTAAGTTACTTCGAATGGGTTCAG                         AACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAG
genomic: AGGAGTCACTGTAAGTTACTTCGAATGGGTTCAGgtatgtatga ... taatgtgcagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAG
EST: gi|116445672|gb|EG488264.1|EG488264
EST:     TATATGCAAACTCTGGAGGAGTCACTGTAAGTTACTTCGAATGGGTTCAG                         AACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAG
genomic: TATATGCAAACTCTGGAGGAGTCACTGTAAGTTACTTCGAATGGGTTCAGgtatgtatga ... taatgtgcagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtactcgaacaaaaccgattttgatcagattagttgtttccggtaatgtgcagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAGACTTACATGACTCGCTCTTTCAAGGACTTGAAAGAGATGTGCAAAACTC
                    ttttgat  putative branch site (score: 4)
                   attttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatgagtctctcaacaacttacctttgacagaccaagtactcgaacaaaaccgattttgatcagattagttgtttccggtaatgtgcagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAGACTTACATGACTCGCTCTTTCAAGGACTTGAAAGAGATGTGCAAAACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG