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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatcctcttagcatttttgatgaagcttcgattctttataaattgagagtatgtaaatgtaaatgaattcatcattttaatgacaatttgtgttgcagCGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGCTGTTGTGAGGAAAGAATGTGCTGCGATCCGTGCTTCGATTAATGAAAAT

Basic information

species Arabidopsis thaliana
transcript AT1G60070.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G60070.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G39930.1 (Glycine max), 3'ss of exon 1
--------agaatcctcttagcatttttgatgaagcttcgattctttataaattgagagtatgtaaatgtaaatgaattcatcattttaatgacaatttgtgt-tgcagCGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGCTGTTGTGAGGAAAGAATGTGCTGCGATCCGTGCTTCGATTAATGAAAAT
         |  |  ||    ||    | || ||  || |    ||||||  || |   |   | | |||       || | || | ||||    || | |   |  || ||||||||||| || ||||||||  | ||||| || || || |||||||||||||| || |||||||||||||| || |||||||| ||  ||||||||
gtagttagtgttttttccccccacaaataataaatgtttg---ttttatagtttaaatatg-atcagtgtct-----tttaacaatctaattcatatctctacatttagGGACATGATTCGGGCCATACGTGCTTGCAAAACTGCAGCAGAAGAACGTGCTGTTGTAAGAAAAGAATGTGCTGCTATTCGTGCTTCAATAGATGAAAAT

upper sequence: AT1G60070.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G03890.1 (Glycine max), 3'ss of exon 1
agaatcctcttagcatttttgatgaagcttcgattctttataaattgaga--gtatgtaaatgtaaatgaattcatc-----attttaatgacaatttgtgttgcagCGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGCTGTTGTGAGGAAAGAATGTGCTGCGATCCGTGCTTCGATTAATGAAAAT
       |   ||       ||| |  | |  ||  | ||||  ||  |   || | ||| | |||   |  || |      || |   | | |       ||| || ||||||||||| || ||||||||  |||| || || || || ||||| |||||||| || |||||||||||||| || |||||| | || |||||||||
-------ttcaagttgcgaagataatacatgtataatatatagtttctgtttgtgtttaattataatcaatatcttttacatatctggttcatatcccaacttgtagGGACATGATTCGGGCCATACGTGCTTGTAAGACTGCAGCAGAAGAACGAGCTGTTGTAAGAAAAGAATGTGCTGCCATTCGTGCTGCAATAAATGAAAAT

upper sequence: AT1G60070.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 1
agaatcctcttagcatttttgatgaagcttcgattctttataaattgagagtatgtaaatgtaaatg---aattcatcatttta---atgacaatt--tgtgttgcagCGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGCTGTTGTGAGGAAAGAATGTGCTGCGATCCGTGCTTCGATTAATGAAAAT
       | ||  | | ||   || |   |  |||||| ||||| | | | | |  || ||   |||   |   |||| | | |   |||   | |  | || || || ||||||||||| ||||| |||||  | |||||||| || ||||||||||||||||| || || ||||||||||| || ||||| ||  | | |||||||
-------tgttttcttcttaagtgga-tattaattcttaataaactaaaattcttaaattgagcatgtttatcccatcgtgtgacatatgtttactattttgatgtagGGACATGATTCGGGCTATCCGTGCTTGCAAAACCGCAGCAGAGGAACGTGCTGTTGTAAGAAAGGAATGTGCTGCTATTCGTGCATCAGTCAGTGAAAAT

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|86064706|gb|DR360463.1|DR360463
EST:     CTTCGTACCGCTCCGGTCATGAATCCATTCTCTTCCGGCACGCGTCTCAG                         CGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGC
genomic: CTTCGTACCGCTCCGGTCATGAATCCATTCTCTTCCGGCACGCGTCTCAGgttaggaatc ... tgtgttgcagCGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGC
EST: gi|86064708|gb|DR360465.1|DR360465
EST:     CTTCGTACCGCTCCGGTCATGAATCCATTCTCTTCCGGCACGCGTCTCAG                         CGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGC
genomic: CTTCGTACCGCTCCGGTCATGAATCCATTCTCTTCCGGCACGCGTCTCAGgttaggaatc ... tgtgttgcagCGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGC
EST: gi|19875009|gb|AU235840.1|AU235840
EST:     CTTCGTACCGCTCCGGTCATGAATCCATTCTCTTCCGGCACGCGTCTCAG                         CGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGC
genomic: CTTCGTACCGCTCCGGTCATGAATCCATTCTCTTCCGGCACGCGTCTCAGgttaggaatc ... tgtgttgcagCGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGC
EST: gi|86064710|gb|DR360467.1|DR360467
EST:     CTTCGTACCGCTCCGGTCATGAATCCATTNTNTTCCGGCACGCGTCTCAG                         CGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGC
genomic: CTTCGTACCGCTCCGGTCATGAATCCATTCTCTTCCGGCACGCGTCTCAGgttaggaatc ... tgtgttgcagCGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGC
EST: gi|86064707|gb|DR360464.1|DR360464
EST:     CTTCGTACCGCTCCGGTCATGAATCCATTCTCTTCCGGCACGCGTCTCAG                         CGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGC
genomic: CTTCGTACCGCTCCGGTCATGAATCCATTCTCTTCCGGCACGCGTCTCAGgttaggaatc ... tgtgttgcagCGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagagtatgtaaatgtaaatgaattcatcattttaatgacaatttgtgttgcagCGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGCTGTTGTGAGGAAAGAATGTGCTGCGATCCGTGCTTCGATTAATGAAAAT
                               ttttaat  putative branch site (score: 3)
          taaatgtaaatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaatcctcttagcatttttgatgaagcttcgattctttataaattgagagtatgtaaatgtaaatgaattcatcattttaatgacaatttgtgttgcagCGACATGATTCGAGCTATACGTGCGAGTAAAACCGCTGCTGAGGAACGTGCTGTTGTGAGGAAAGAATGTGCTGCGATCCGTGCTTCGATTAATGAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
agaatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgacaa