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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgagatctaacatagagtgttttcttgttagtagatcactttagtttttttctgatgaactttgtttagGTTTTACGCGGCGGATGTGAGGAAAGACAGTTTTGAGGTGTTTGATAAGTGTAAGAGAAAAGTGGTAGTGACGGCGAATCCGATTGTGATGGTGGAGGCG

Basic information

species Arabidopsis thaliana
transcript AT4G00400.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G00400.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G07580.1 (Glycine max), 3'ss of exon 1
gtacgagatctaacatagagtgttttcttgttagtagatcactttagtttttttctgatgaactttgtttagGTTTTACGCGGCGGATGTGAGGAAAGACAGTTTTGAGGTGTTTGATAAGTGTAAGAGAAAAGTGGTAGTGACGGCGAATCCGATTGTGATGGTGGAGGCG
       | || ||  |     |||  || |   ||  ||  ||  || || |  |   |   |  ||  |||||||| || |||||||||||||| || || || |||||||| ||   ||| ||||| || || || ||||||||||||||||   ||||||||||| ||
-----gtaactcactcactcgatttctttctc--tacttcgtttctgtgttctgatcgcgcg-tgagtgcagGTTTTATGCTGCGGATGTGAGGAAGGAGAGCTTCGAGGTGTTCGACCGGTGCAAGAGGAAGGTCGTGGTGACGGCGAATCCGACGCTGATGGTGGAGCCG
















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|19876550|gb|AU237381.1|AU237381
EST:     GGTCTCAAAATCCGCGATATCGAACTTGTCTCTCGCGCAGTTCTTCCACG                         GTTTTACGCGGCGGATGTGAGGAAAGACAGTTTTGAGGTGTTTGATAAGTG
genomic: GGTCTCAAAATCCGCGATATCGAACTTGTCTCTCGCGCAGTTCTTCCACGgtacgagatc ... ctttgtttagGTTTTACGCGGCGGATGTGAGGAAAGACAGTTTTGAGGTGTTTGATAAGTG
EST: gi|125198412|gb|EL213366.1|EL213366
EST:     GGTCTCAAAATCCGCGATATCGAACTTGTCTCTCGCGCAGTTCTTCCACG                         GTTTTACGCGGCGGATGTGAGGAAAGAACAGTTTTGAGGTGTTTGATAAGT
genomic: GGTCTCAAAATCCGCGATATCGAACTTGTCTCTCGCGCAGTTCTTCCACGgtacgagatc ... ctttgtttagGTTTTACGCGGCGGATGTGAGGAAAGA-CAGTTTTGAGGTGTTTGATAAGT
EST: gi|124850333|gb|EH934770.1|EH934770
EST:     CGCAGTTCTTCCACG                         GTTTTACGCGGCGGATGTGAGGAAAGACAGTTTTGAGGTGTTTGATAAGTG
genomic: CGCAGTTCTTCCACGgtacgagatc ... ctttgtttagGTTTTACGCGGCGGATGTGAGGAAAGACAGTTTTGAGGTGTTTGATAAGTG
EST: gi|124758641|gb|EH848771.1|EH848771
EST:     GGCCTCAAAATCCGCGATATCGAACTTGTCTCTCGCGCAGTTCTTCCACG                         GTTTTACGCGGCGGA
genomic: GGTCTCAAAATCCGCGATATCGAACTTGTCTCTCGCGCAGTTCTTCCACGgtacgagatc ... ctttgtttagGTTTTACGCGGCGGA
EST: gi|125045186|gb|EL117455.1|EL117455
EST:     CAAAATCCGCGATATCGAACTTGTCTCTCGCGCAGTTCTTCCACG                         GTTTTACGCGGCGGATGTGAGGAAAGACAGTTTTGAGGTGTTTGATAAGTG
genomic: CAAAATCCGCGATATCGAACTTGTCTCTCGCGCAGTTCTTCCACGgtacgagatc ... ctttgtttagGTTTTACGCGGCGGATGTGAGGAAAGACAGTTTTGAGGTGTTTGATAAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtgttttcttgttagtagatcactttagtttttttctgatgaactttgtttagGTTTTACGCGGCGGATGTGAGGAAAGACAGTTTTGAGGTGTTTGATAAGTGTAAGAGAAAAGTGGTAGTGACGGCGAATCCGATTGTGATGGTGGAGGCG
                                   ttctgat  putative branch site (score: 3)
                                             ctttgttt  putative PPT
                       actttagttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgagatctaacatagagtgttttcttgttagtagatcactttagtttttttctgatgaactttgtttagGTTTTACGCGGCGGATGTGAGGAAAGACAGTTTTGAGGTGTTTGATAAGTGTAAGAGAAAAGTGGTAGTGACGGCGAATCCGATTGTGATGGTGGAGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG