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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgactctgatctcacagatctcatccctagttattttggttgattagagtctcaatcccaagttatttccttgtcccttgtatttctcctatttttatacttgattattttgacaatctttctttatagGGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTG

Basic information

species Arabidopsis thaliana
transcript AT4G39460.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39460.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G15150.1 (Glycine max), 3'ss of exon 4
gtaagtgactctgatctcacagatctcatccctagttattttg-gttgattagagtctcaatcc-caagttatttccttgtcccttgtatttctcctatttttatacttgattattttgacaatctttctttatagGGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTG
                       | |||    |  | ||||   | | || |   | | ||| |   |   |  ||   || | ||   |  | ||| | |          ||  ||| | |       | |  ||||| || |||||||||||||||||||| ||||| | |||||||||| |||||| ||  |||||||| ||  |||| ||  || ||||  ||
--------------------gattttcacaagttttcatttcatgcttatcaagatatgaatgcatgaaacacatctaggttctttccttcacacctttct---------gttgcttttaaa-------tatgcagGGCATCTGCTTTATTTGTTGGAGTTTATGAACCTATAAAGCAGAAATTGCTGAGGATATTTCCTGAACACCTAAGTGCTTTTACTCATTTG

upper sequence: AT4G39460.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G31870.1 (Glycine max), 3'ss of exon 5
gtaagtgactctgatctcacagatctcatccctagttattttg-gttgattagagtctcaatcc-caagttatttccttgtcccttgtatttctcctatttttatacttgattattttgacaatctttctttatagGGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTG
                       | |||    |  | ||||   | | || ||  | | ||| |   | | |  ||   || | ||  ||  | ||  |||          ||  ||| | |       | |  ||||| || |||||||||||||||||||| ||||| | |||||||||| |||||| |   |||||||| ||  | || ||  || ||||| ||
--------------------gattttcacaagttttcatttcatgcttatcaggatatgaattcatgaatcacatctaggttctttccatcacaccctttt---------gttgcttttaaa-------tatgcagGGCATCTGCTTTATTTGTTGGAGTTTATGAACCTATAAAGCAGAAATTGCTGAGGGTATTTCCTGAACACCTGAGTGCTTTTACTCACTTG
















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|86037549|gb|DR333304.1|DR333304
EST:     TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACC                         GGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT
genomic: TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACCgtaagtgact ... ttctttatagGGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT
EST: gi|86037541|gb|DR333296.1|DR333296
EST:     TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACC                         GGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT
genomic: TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACCgtaagtgact ... ttctttatagGGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT
EST: gi|86037538|gb|DR333293.1|DR333293
EST:     TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACC                         GGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT
genomic: TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACCgtaagtgact ... ttctttatagGGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT
EST: gi|86037540|gb|DR333295.1|DR333295
EST:     TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACC                         GGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT
genomic: TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACCgtaagtgact ... ttctttatagGGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT
EST: gi|86037532|gb|DR333287.1|DR333287
EST:     TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACC                         GGCTTCGGCTTTATTTGTTGGA
genomic: TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACCgtaagtgact ... ttctttatagGGCTTCGGCTTTATTTGTTGGA
EST: gi|86037555|gb|DR333310.1|DR333310
EST:     TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACC                         GGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT
genomic: TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACCgtaagtgact ... ttctttatagGGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT
EST: gi|124927607|gb|EL005330.1|EL005330
EST:     TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACC                         GGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAG
genomic: TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACCgtaagtgact ... ttctttatagGGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAG
EST: gi|86037534|gb|DR333289.1|DR333289
EST:     TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACC                         GGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT
genomic: TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACCgtaagtgact ... ttctttatagGGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT
EST: gi|86037548|gb|DR333303.1|DR333303
EST:     TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACC                         GGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT
genomic: TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACCgtaagtgact ... ttctttatagGGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT
EST: gi|86037553|gb|DR333308.1|DR333308
EST:     TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACC                         GGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT
genomic: TTGAAGGGTCTTTATTCAGGATTAGCTGGAAATATCGCTGGTGTCTTACCgtaagtgact ... ttctttatagGGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttgtatttctcctatttttatacttgattattttgacaatctttctttatagGGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTG
                                 ttttgac  putative branch site (score: 3)
                                          tctttctttat  putative PPT
               tatttttatacttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgactctgatctcacagatctcatccctagttattttggttgattagagtctcaatcccaagttatttccttgtcccttgtatttctcctatttttatacttgattattttgacaatctttctttatagGGCTTCGGCTTTATTTGTTGGAGTTTACGAACCCACAAAGCAGAAACTGCTGAAGACCTTTCCTGATCATTTAAGCGCAGTTGCTCACCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA