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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcgatttatatgttttactgagaaattagagcttactgatgtgtgctgttgaatctgactaattgcatttatggaattggacatggttttaataatagGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAG

Basic information

species Arabidopsis thaliana
transcript AT2G47470.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g23740.1 (Oryza sativa), 3'ss of exon 1
tttcgatttatatgttttactgagaaattagagcttactgatgtgtgctgttgaatctg-actaattgcatttatggaattggacatggttttaataat------agGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAG
       | | |||| |||||   |||     |||||   || |||||  |    || | | |      || | | |  ||   ||| | | ||   ||      |||||||||||||||||||| ||||| || |||||||||||||| || ||||| |||||||| || || ||||| || |||||||||
------ctcagatgtattactagaaaaaccatgcttaaatatttgtgc-atcagttcagcatttcaaagatatctagtgttactcatcggtctatctatctggttagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAGTATGAAAAGCTTGGTGCAAGTTTCAAGAAAGCCAAATCTGTCTTTATTGCAAAG

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 1
---tttcgatttatatgttttactga--gaaattagagcttactgatgtgtgctgttgaatctgactaattgcatttatggaattggacatggttttaataatagGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAG
   |||    |||||| ||    ||   |   || | |     |  | |||   |   |||  || || ||   ||||     |||    || ||||  |   |||||||||||||||||||| ||||| || || || ||||| || || ||||| |||||||| || || || ||  | ||||| |||
ggcttttatgttatatcttgcggtggttggtgttgggggagggtt-tatgtatagagaaattcga-tattt---tttaaatgtttgtgattgattttgttttcagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAGTTTCAAGAAAGCCAAATCAGTCCTAATTGCGAAG

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G128171_T03 (Zea mays), 3'ss of exon 1
tttcgatttatatgttttactgagaaattagagcttactgatgtgtgctgttgaa--tctgactaattgcatttatggaattggacatggttttaataat-agGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAG
     |  || |   | ||||  ||| |||    ||       |  || | | ||  | | |  ||||    || |     |   | || |||   |  | |||||||||||||||||||| |||||||| ||||||||||  || || ||||| || ||||| ||||| ||||| |||||||| |||
--gtaacataga-actgtacttggaatttattatttctctgcatcagcaggtcaacgtttcataaattctggttttaatcatctgcttgatttgtttgtttagGTGTGGTCACTGCAAGAAGCTTGCTCCTGAGTATGAAAGACTTGGTGCAAGTTTTAAGAAAGCTAAATCTGTCTTGATTGCTAAG

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G159369_T01 (Zea mays), 3'ss of exon 1
-tttcgatttatatgttttactgagaaattagagcttactgatgtgtgctgttgaatctgactaattgcatttatggaattggacatggttttaataatagGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAG
 | |      | ||   |||    ||||        |    || |||  |  ||| |||   || | |    | |     ||   ||  | |   |  ||||||||| |||||||| || ||||| || ||||||||||| || || || ||||||||||||||||| |||||  |||| ||||||
ctgtgagcacaaatcacttatctggaaacctttctatgaccatttgttttagtga-tctttttattggttactctttttctgactatcttctgtttcttagGTGTGGCCACTGCAAAAAGCTTGCCCCCGAGTATGAAAAACTTGGCGCCAGCTTCAAGAAGGCTAAATCTGTACTGATAGCAAAG

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G01750.1 (Glycine max), 3'ss of exon 1
tttcgatttatatgttttactgagaaattag-agcttactgatgtgtgctgttgaatctgac---taattgcatttatggaattggacatggttttaataatagGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAG
  |  |  |||   || || | |  | | || | ||| || || | |  | |  |  || |    | |||   |||| | |      | |  || |  |||||||||||| |||||||| || ||||||||||| ||||||||||| ||    ||||||||||| || || ||||| || || |  |||
--ttaacctattcattgtagtaattactaagtaacttccttatat-tagtatgtacactaatatgtcattatgtttacg-atcacttcctctttgttgtaatagGTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG

upper sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G01820.1 (Glycine max), 3'ss of exon 2
tttcgatttatatgttttactgagaaattag-agcttactgatgt-gtgctgttgaatc-tgactaattgcatttatggaattggacatggttttaataatagGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAG
     |   ||   || |||| |  | |||| |  || || ||||  |  |||| | |  |   | |||   |||| |        | |  || |  |||||||||||| |||||||| || ||||||||||| ||||||||||| ||    ||||||||||| || || ||||| || ||||  |||
---taaccaattcattgtactaattacttagtaatttccttatgttattatgttcactaatatgtcattatgtttacgatcacttccttttttgttgtaatagGTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG

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|116441306|gb|EG483898.1|EG483898
EST:     AAGGAAGTTGGTAAAGATAAAGGAGCTCTCGTCGAGTTTTACGCTCCCTG                         GTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAG
genomic: AAGGAAGTTGGTAAAGATAAAGGAGCTCTCGTCGAGTTTTACGCTCCCTGgtatggttca ... ttaataatagGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAG
EST: gi|125255289|gb|EL269374.1|EL269374
EST:     AAGGAAGTTGGTAAAGATAAAGGAGCTCTCGTCGAGTTTTACGCTCCCTG                         GTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAG
genomic: AAGGAAGTTGGTAAAGATAAAGGAGCTCTCGTCGAGTTTTACGCTCCCTGgtatggttca ... ttaataatagGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAG
EST: gi|164033510|gb|ES033892.1|ES033892
EST:     GGAAGTTGGTAAAGATAAAGGAGCTCTCGTCGTAGTTTTACGCTCCCTG                         GTGTGGTCACTGCAAGAAAC
genomic: GGAAGTTGGTAAAGATAAAGGAGCTCTCGTCG-AGTTTTACGCTCCCTGgtatggttca ... ttaataatagGTGTGGTCACTGCAAGAAAC
EST: gi|125204837|gb|EL219791.1|EL219791
EST:     AAGGAAGTTGGTAAAGATAAAGGAGCTCTCGTCGAGTTTTACGCTCCCTG                         GTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGC
genomic: AAGGAAGTTGGTAAAGATAAAGGAGCTCTCGTCGAGTTTTACGCTCCCTGgtatggttca ... ttaataatagGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGC
EST: gi|124842175|gb|EH926612.1|EH926612
EST:     CGAGTTTTACGCTCCCTG                         GTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAGAGCTAGGGGCAAG
genomic: CGAGTTTTACGCTCCCTGgtatggttca ... ttaataatagGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAG
EST: gi|301501187|gb|HO206727.1|HO206727
EST:     AAGGAAGTTGGTAAAGATAAAGGAGCTCTCGTCGAGTTTTACGCTCCCTG                         GTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAG
genomic: AAGGAAGTTGGTAAAGATAAAGGAGCTCTCGTCGAGTTTTACGCTCCCTGgtatggttca ... ttaataatagGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgttgaatctgactaattgcatttatggaattggacatggttttaataatagGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAG
                                       atggttttaataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcgatttatatgttttactgagaaattagagcttactgatgtgtgctgttgaatctgactaattgcatttatggaattggacatggttttaataatagGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG