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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctttttcgtgaaatctcctttgttctatatgagtatttctagttgttgcaagtaatcatctaacgagatttgttgtttttgttattgctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAAAGAAGCTAGATGATGATACTGAGAACTTATCTC

Basic information

species Arabidopsis thaliana
transcript AT3G58680.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G58680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G42890.1 (Glycine max), 3'ss of exon 1
tttctttttcgtgaaatctcctttgttctatatgagtatt-tctagttgttgcaagtaatcatcta-acgagatttgttgtttttgttattgctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAAAGAAGCTAGATGATGATACTGAGAACTTATCTC
| |||| |  ||      |  |||  ||  | | | | || | | |||| |     |  | || |  | |   |    |||  |||||     | | |  ||  ||||||||  | ||||| || ||||| |||||||| || |||||||| |||| ||| ||||||||||||||||   || |||
tgtcttatgtgtttgtgtttttttaatcgtttttattcttcttttgttgataagcttttttatttggatggtttgaactgtgattgtt--caattgttacagATAATGCTGGGACAAACAAAGCAGCATCTAGCGGCACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAGTCTAGCTC

upper sequence: AT3G58680.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G15420.1 (Glycine max), 3'ss of exon 1
-tttctttttcgtgaaatctcctttgttctatatgagtatttctagttgttgcaagtaatcatctaacgagatttgttgtttttgttattgctg--ggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAAAGAAGCTAGATGATGATACTGAGAACTTATCTC
  ||  |||   |   ||||  ||||||||   |  || |    || | ||  |  |       |   ||  | || |  ||   || ||| ||  | |  ||  ||||||||  | || || || ||||| ||| |||| || |||||||| |||| ||| |||||||||||||||||  || |||
tgtttgtttctttttgatcttttttgttcttcttttgt-tgataagcttttttatttggatggtt--tgaattgtgattgttcaattgttgttgttgttacagATAATGCTGGGACAAATAAAGCAGCATCTAGCAGCACTTCATTGAACACTAAGAGGCTGGATGATGATACTGAGAATCTAGCTC
















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|86060838|gb|DR356595.1|DR356595
EST:     TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAAT                         TCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
genomic: TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAATgtttgttttc ... ctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
EST: gi|86060848|gb|DR356605.1|DR356605
EST:     TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAAT                         TCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
genomic: TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAATgtttgttttc ... ctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
EST: gi|86080667|gb|DR376424.1|DR376424
EST:     TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAAT                         TCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
genomic: TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAATgtttgttttc ... ctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
EST: gi|164143842|gb|ES061963.1|ES061963
EST:     CAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAAT                         TCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
genomic: CAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAATgtttgttttc ... ctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
EST: gi|164118901|gb|ES045541.1|ES045541
EST:     CAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAAT                         TCAATGCTGGATCGAACAAGGCTGACAATCAAGCGGCACCTCCTTGAACAC
genomic: CAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAATgtttgttttc ... ctgggtttagTCAATGCTGGATCGAACAAGGCTG-CA-TCAAGCGGCACCTCCTTGAACAC
EST: gi|47830185|gb|CK119869.1|CK119869
EST:     TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAAT                         TCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
genomic: TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAATgtttgttttc ... ctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
EST: gi|86060844|gb|DR356601.1|DR356601
EST:     TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAAT                         TCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
genomic: TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAATgtttgttttc ... ctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
EST: gi|125089824|gb|EL148049.1|EL148049
EST:     TCGTCGAAGCGGCGCCGATATTGAGACCGTTCG-AAAT                         TCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAA
genomic: TCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAATgtttgttttc ... ctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAA
EST: gi|86060842|gb|DR356599.1|DR356599
EST:     TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAAT                         TCAATGCTGGATCGAACAAGGCTGCATCAAGCGGNACCTCCTTGAACACAA
genomic: TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAATgtttgttttc ... ctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
EST: gi|86060846|gb|DR356603.1|DR356603
EST:     TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAAT                         TCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
genomic: TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAATgtttgttttc ... ctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
EST: gi|125280245|gb|EL294330.1|EL294330
EST:     GCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAAT                         TCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
genomic: GCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAATgtttgttttc ... ctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
EST: gi|47831590|gb|CK121274.1|CK121274
EST:     TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAAT                         TCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
genomic: TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAATgtttgttttc ... ctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
EST: gi|47831671|gb|CK121355.1|CK121355
EST:     CAACGCNNNCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAAT                         TCAATGCTGGATCGAACAAG
genomic: CAACGC---CGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAATgtttgttttc ... ctgggtttagTCAATGCTGGATCGAACAAG
EST: gi|86060849|gb|DR356606.1|DR356606
EST:     TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAAT                         TCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA
genomic: TGTCAACGCCGCTCGTCGAAGCGGCGCCGATATTGAGACCGTTCGAAAATgtttgttttc ... ctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgcaagtaatcatctaacgagatttgttgtttttgttattgctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAAAGAAGCTAGATGATGATACTGAGAACTTATCTC
               atctaac  putative branch site (score: 2)
                              ttgtttttgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctttttcgtgaaatctcctttgttctatatgagtatttctagttgttgcaagtaatcatctaacgagatttgttgtttttgttattgctgggtttagTCAATGCTGGATCGAACAAGGCTGCATCAAGCGGCACCTCCTTGAACACAAAGAAGCTAGATGATGATACTGAGAACTTATCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - -tgaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - -caagtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacgaga