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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgagtgaaacccccattagtcacattagcagaagcaagtttttctttggttgctgacaatgtttttgtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTATTCCCTACTTTAGTGGCGCTGCTTATGTCTATGAACATTTTGTGAGACCG

Basic information

species Arabidopsis thaliana
transcript AT1G74520.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G74520.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G10730.1 (Glycine max), 3'ss of exon 3
-----gtaagatgagtgaaacccccattagtcacattagcagaag--caagttttt---ctttggttg----ctgacaatgtttttgtgtga-----tcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTATTCCCTACTTTAGTGGCGCTGCTTATGTCTATGAACATTTTGTGAGACCG
      |  | || |  |||     || ||| | |  |||| | |   |||| |||    ||||| ||     | ||||  | | | | |       ||||| | || |||||| | ||    ||||||||    || |||||| | ||  |||| |||||||| || ||||||||||| ||||| |||| ||||||||| 
atgagttctgttgtggcaaatatatat-agttagaagagcacagggtaaagtatttaacttttggctgaattttcacaacatatgtatatatgtatttcagGATTCCAATATGGCCTTATGCAAAGCTGATTGCAACCTGCTGGTTGGTCCTTCCTTACTTTAGCGGTGCTGCTTATGTTTATGAGCATTATGTGAGACCT

upper sequence: AT1G74520.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 3
-------gtaagatgagtg-aaacccccattagtcaca-----ttagcaga------agcaagtttttctttggttgctgacaatgtttttgtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTATTCCCTACTTTAGTGGCGCTGCTTATGTCTATGAACATTTTGTGAGACCG
        |  ||| | |      ||   || || |       ||| | ||      || || |    || || |||   |   ||| | ||||||  |||| | ||  | ||| ||||    ||||||||    ||||||||| | || || |||||||| ||||| ||||| ||||| ||||| |||||||||||||| 
aaattgaatgggatcaatttgggtcctttttggtaattctgttttatctgagatatcagaaactacacctctgcttgaacatgttgtgtctgtgtgg-cagGCTCCCTTTTTGGCCATATGCAAAGCTGATTGCAACTTGCTGGTTGGTCATACCCTACTTCAGTGGTGCTGCATATGTTTATGAGCATTTTGTGAGACCT
















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|86052442|gb|DR348199.1|DR348199
EST:     TATTCATTACTTACACTCATCGAACTCACATTCGCCAAACTCATCGAATG                         GTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
genomic: TATTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
EST: gi|86052429|gb|DR348186.1|DR348186
EST:     TATTCATTACTTACACTCATCGAACTCACATTCGCCAAACTCATCGAATG                         GTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
genomic: TATTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
EST: gi|124897282|gb|EH973496.1|EH973496
EST:     TATTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATG                         GTTACCGATATGGTCATACATGAAGCTGATCTTGACTTG
genomic: TATTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTG
EST: gi|86052441|gb|DR348198.1|DR348198
EST:     TATTCATTACTTACACTCATCGAACTCACATTCGCCAAACTCATCGAATG                         GTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
genomic: TATTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
EST: gi|86052439|gb|DR348196.1|DR348196
EST:     TATTCATTACTTACACTCATCGAACTCACATTCGCCAAACTCATCGAATG                         GTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
genomic: TATTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
EST: gi|125021986|gb|EL094255.1|EL094255
EST:     CATTCGCCAAACTCATCGAATG                         GTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
genomic: CATTCGCCAAACTCATCGAATGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
EST: gi|86052433|gb|DR348190.1|DR348190
EST:     TATTCATTACTTACACTCATCGAACTCACATTCGCCAAACTCATCGAATG                         GTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
genomic: TATTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
EST: gi|86052431|gb|DR348188.1|DR348188
EST:     TATTCATTACTTACACTCATCGAACTCACATTCGCCAAACTCATCGAATG                         GTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
genomic: TATTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
EST: gi|125252231|gb|EL266316.1|EL266316
EST:     ATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATG                         GTTACCGATATGGCCATACATGAAGCTGATCTTGACTTGCTGG
genomic: ATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGG
EST: gi|86052443|gb|DR348200.1|DR348200
EST:     TATTCATTACTTNCACTCATCGAACTCACATTCGCCAAACTCATCGAATG                         GTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
genomic: TATTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
EST: gi|86052432|gb|DR348189.1|DR348189
EST:     TATTCATTACTTACACTCATCGAACTCACATTCGCCAAACTCATCGAATG                         GTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
genomic: TATTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
EST: gi|19878871|gb|AU239702.1|AU239702
EST:     TATTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATG                         GTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
genomic: TATTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
EST: gi|86052438|gb|DR348195.1|DR348195
EST:     TATTCATTACTTACACTCATCGAACTCACATTCGCCAAACTCATCGAATG                         GTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
genomic: TATTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
EST: gi|125236287|gb|EL250372.1|EL250372
EST:     TCGAGCTCACATTCGCCAAACTCATCGAATG                         GTTACCGATATCGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
genomic: TCGAGCTCACATTCGCCAAACTCATCGAATGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
EST: gi|86052440|gb|DR348197.1|DR348197
EST:     TATTCATTACTTACACTCATCGAACTCACATTCGCCAAACTCATCGAATG                         GTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
genomic: TATTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATCGAATGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTAT
EST: gi|125261193|gb|EL275278.1|EL275278
EST:     TTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCATACGAAATG                         GTTACCGATATGGTCATACATGAA
genomic: TTCATTACTTACACTCATCGAGCTCACATTCGCCAAACTCAT-CGAA-TGgtaagatgag ... gtgtgatcagGTTACCGATATGGTCATACATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattagcagaagcaagtttttctttggttgctgacaatgtttttgtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTATTCCCTACTTTAGTGGCGCTGCTTATGTCTATGAACATTTTGTGAGACCG
                             tgctgac  putative branch site (score: 2)
                                        tttttgt  putative PPT
                 tttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatgagtgaaacccccattagtcacattagcagaagcaagtttttctttggttgctgacaatgtttttgtgtgatcagGTTACCGATATGGTCATACATGAAGCTGATCTTGACTTGCTGGCTTGTTATTCCCTACTTTAGTGGCGCTGCTTATGTCTATGAACATTTTGTGAGACCG

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