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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggttcagcaaatagttgtgttagcatattgtataattcttgtgaatcccaaattgcactttctctggattgttgtctaatattggtctcaacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGCAAACCCAAGACAGTTCAAGATTCCAGACTGGTTTTTGAACAGACAGAAA

Basic information

species Arabidopsis thaliana
transcript AT1G34030.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G34030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G36880.2 (Glycine max), 3'ss of exon 2
aggttcagcaaatagttgtgttagcatattgtataattcttgtgaatc-ccaaattgcactttctctggattgttgtctaatattgg-tctcaacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGCAAACCCAAGACAGTTCAAGATTCCAGACTGGTTTTTGAACAGACAGAAA
                ||  ||    |||||  | | |    |   ||   || | |||| || |   | || ||||  ||  | || | |    || ||||||||||||||||  |||| |||||| | ||||   | |||||| | || || ||||| || ||||||||||| ||| ||||||||||||||||| |||| 
---------------gtgcttttttttattggttgagttcaattgctcgttaattcgcacatttttgtggttattgttgaaattgggatttttgtttgtcagGGCTGGTGAGTTGACTGCTGCTGAGTTGGACAGTGTGATGACTGTGGTGGCGAACCCTAGGCAGTTCAAGATCCCAAACTGGTTTTTGAACAGAAAGAAG

upper sequence: AT1G34030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G36610.3 (Glycine max), 3'ss of exon 2
aggttcagcaaatagttgtgttagcatattgtataattcttgtgaatc-ccaaattgcactttctctggattgttgtctaatattgg-tctcaacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGCAAACCCAAGACAGTTCAAGATTCCAGACTGGTTTTTGAACAGACAGAAA
                ||  ||    |||||  | | |    |   ||   || | |||| || |   | || ||||  ||  | || | |    || ||||||||||||||||  |||| |||||| | || |   | |||||| | || || ||||| || ||||||||||| ||||||||||||||||||||| |||| 
---------------gtgcttttttttattggttgagttcaattgctcgttaattcgcacatttttgtggttattgttgaaattgggatttttgtttgtcagGGCTGGTGAGTTGACTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTGGCGAACCCTAGGCAGTTCAAGATCCCAGACTGGTTTTTGAACAGAAAGAAG

upper sequence: AT1G34030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------aggttcagcaaatagttgtgttagcatattgtataattcttgtgaatcccaaattgcactttctctggattgttgtctaata----ttggtctcaactttt--cagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGCAAACCCAAGACAGTTCAAGATTCCAGACTGGTTTTTGAACAGACAGAAA
                                                               | | ||  | |  |||||| |   ||      |   |  ||          |||    |||   ||  ||||  |  |||     |||||      | ||  ||| ||||||||  |   ||| |||||| | || |   | |||||| | ||||| |||||  | || ||||||||||| |||||||||||||||||| |||| 
gtttgctttactttcattgccattattgttgttttcattgttagttaataatatttgtttattgttgcataagagtgttgtggttcaattggaatttgctgctgcttgctgtggatttggtttttcatgttttgtattgaaatgggctttggttatttttgttggcagAGCTGGTGAACTGAGTGCTGCTGAGTTGGATAGTGTGATGACTGTGGTTGCCAACCCCCGGCAATTCAAGATTCCGGACTGGTTTTTGAACAGAAAGAAG

upper sequence: AT1G34030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv18s0072g00060.t01 (Vitis vinifera), 3'ss of exon 3
--aggttcagcaaatagttgtgttagcatattgtataattcttgtgaatcccaaattgcactttctctggattgttgtctaatattggtctcaacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGCAAACCCAAGACAGTTCAAGATTCCAGACTGGTTTTTGAACAGACAGAAA
   || |    |  ||  | |||    || || | ||  | |      |      || ||     ||||  ||| | ||| | |||||| | |   | ||||||||||||| |||||||| |||||| | || |||||||||  ||||||||| || || || || ||||| ||||| |||||||||||||| ||  | || 
gagggattcatatttatgtttgtctttatgtt-tttatctgtaacatgttaagtttttcaaagcatctgatttgctatctga-attggtttaatgctctcagGGCTGGTGAATTATCTGCTGCTGAGCTGGAGAACCTCATGGTTATTGTTGCTAATCCTAGGCAATTCAAAATTCCTGACTGGTTTTTGAATAGGAAAAAG

upper sequence: AT1G34030.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S215_81V6.1 (Physcomitrella patens), 3'ss of exon 2
--aggttcagcaaatagttgtgttagcatattgtataattcttgtgaatcccaaattgcactttctctggattgttgtctaatattggtctca----acttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGCAAACCCAAGACAGTTCAAGATTCCAGACTGGTTTTTGAACAGACAGAAA
      ||    || ||      | | ||  | | || || |||| ||       || |  ||| |  | |||||  |||||| || ||||      | | ||||| || |||||| | || ||||| ||| | || ||| | |||   |||||||| |||||  | ||||||||||||||||| |||||| | |||||| |||||
tacttctccctgaacagcgac--tcggatcctct-tatttattgtaaaattgtggtt-cgattttttagtattgt--tctaattttagtcttcttttattcttcagAGCCGGTGAGCTCTCCGCAGCAGAGCTGGAGAACTTGATGGTGATTGTTGCTAACCCTCGCCAGTTCAAGATTCCAGATTGGTTTCTTAACAGAAAGAAA

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|124867273|gb|EH951710.1|EH951710
EST:     TGCAAGAAAGCCGATGTCGACATGAACAAGAG                         GGCTGGTGAGTTATCTGCAGCTGAGA
genomic: TGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTATCTGCAGCTGAGA
EST: gi|125133658|gb|EL175012.1|EL175012
EST:     AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAG                         GGCTGGTGAGTTATCTGCAGCTGAGATTGAC
genomic: AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGAC
EST: gi|124866459|gb|EH950896.1|EH950896
EST:     AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAG                         GGCTGGTGAGTTATCTGCA
genomic: AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTATCTGCA
EST: gi|124881436|gb|EH960338.1|EH960338
EST:     AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAG                         GGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCT
genomic: AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCT
EST: gi|86081873|gb|DR377632.1|DR377632
EST:     AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAG                         GGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGC
genomic: AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGC
EST: gi|124990246|gb|EL062515.1|EL062515
EST:     AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAG                         GGCTGGTGAGTTATCTGCAGCTGAGATTGACAAC
genomic: AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAAC
EST: gi|125300738|gb|EL314823.1|EL314823
EST:     CCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAG                         GGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTAT
genomic: CCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTAT
EST: gi|125123338|gb|EL169787.1|EL169787
EST:     CCGATGTCGACATGAACAAGAG                         GGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGC
genomic: CCGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGC
EST: gi|125084441|gb|EL144646.1|EL144646
EST:     AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAG                         GGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCA
genomic: AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCA
EST: gi|124771015|gb|EH861145.1|EH861145
EST:     CGATGTCGACATGAACAAGAG                         GGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGC
genomic: CGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGC
EST: gi|86081156|gb|DR376913.1|DR376913
EST:     AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAG                         GGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGC
genomic: AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGC
EST: gi|86078529|gb|DR374286.1|DR374286
EST:     AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAG                         GGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGC
genomic: AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGC
EST: gi|124763718|gb|EH853848.1|EH853848
EST:     AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAG                         GGCTGGTGAGTTATCTGCAGCT
genomic: AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTATCTGCAGCT
EST: gi|164231891|gb|ES021647.1|ES021647
EST:     AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAG                         GTCTGGTGAGTTATCTGCA
genomic: AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTATCTGCA
EST: gi|124809880|gb|EH895222.1|EH895222
EST:     AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAG                         GGCTGGTGAGTTATACTGCAGCTGAGATTGACAACCTC
genomic: AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTAT-CTGCAGCTGAGATTGACAACCTC
EST: gi|47827960|gb|CK117644.1|CK117644
EST:     AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAG                         GTCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGC
genomic: AGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtattgattt ... aacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcccaaattgcactttctctggattgttgtctaatattggtctcaacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGCAAACCCAAGACAGTTCAAGATTCCAGACTGGTTTTTGAACAGACAGAAA
                             gtctaat  putative branch site (score: 3)
                                               cttttc  putative PPT
                              tctaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggttcagcaaatagttgtgttagcatattgtataattcttgtgaatcccaaattgcactttctctggattgttgtctaatattggtctcaacttttcagGGCTGGTGAGTTATCTGCAGCTGAGATTGACAACCTCATGACTATTGTTGCAAACCCAAGACAGTTCAAGATTCCAGACTGGTTTTTGAACAGACAGAAA

- - -cagcaaa
- - - - - - - - - - - - - - - - - - - - - - - - ccaaatt