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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtgttttaatgtggttgtctgtgttcttatctgttgtatagtgtgttcatgatttgaagatgatgctagcaatcctttaataccctgttggtttgcttcatgaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCTGGTTTCCACAAAGAGAACAAGCAACTTGATGCTGAAATCCACAGGAACT

Basic information

species Arabidopsis thaliana
transcript AT5G39740.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g67134.1 (Oryza sativa), 3'ss of exon 6
----------------------------------------gta-ttgtgttttaatgtggttgtctgtgttcttatctgttgtatag-tgtgttcatgatttgaagatgatgctagcaatcctttaata-----ccctgttggtttgcttc---atgaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCTGGTTTCCACAAAGAGAACAAGCAACTTGATGCTGAAATCCACAGGAACT
                                         || |||  || | |  ||    ||    | || | || || || |        | | |    ||  |   | | |     || || ||      | ||| | | | ||||    |    ||  ||||||||||||| || |||||||| || ||||||||||||||||| |||||||| ||| | || ||  | ||||| |||||| |||| || ||| | || |
gtgtgttgtgctttgatcgcaactgttggctgctgtaataatagttgatttatcacttgaacatcaaattcctcagctcttttagaaacacaaccgttacgataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttttcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGT

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g67126.1 (Oryza sativa), 3'ss of exon 6
----------------------------------------gta-ttgtgttttaatgtggttgtctgtgttcttatctgttgtatag-tgtgttcat-gatttgaagatgatgctagcaatcctt--taata--ccctgttggtttgcttca-tgaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCTGGTTTCCACAAAGAGAACAAGCAACTTGATGCTGAAATCCACAGGAACT
                                         || |||  || | |  ||    ||    |  | | || || || |        | |  || | |   |     |    |||  |  || ||   | ||| | | | ||||  |    ||  ||||||||||||| || |||||||| || ||||||||||||||||| |||||||| ||| | || ||  | ||||| |||||| |||| || ||| | || |
gtgtgttgtgctttgatctcaactgttggctgctgtaataatagttgatttgtcacttgaacatcaaattcatcagctcttttagaaacacaaccgtcaatataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGT

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G815894_T03 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------gtattgtgttttaatgtggttgtctgtgttcttatctgttgtatagtgtgttcatgatttgaagatgatgctagcaatcctttaataccctgttggtt--tgcttcatgaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCTGGTTTCCACAAAGAGAACAAGCAACTTGATGCTGAAATCCACAGGAACT
                                                             |||   |  ||||     | | | ||     |  ||||||| |  |  |   | ||  |  ||      |  ||   || || |    |   | ||  ||| | |||   ||  ||||||||||||| || || || ||||| |||||||| || ||||| |||||||||||| | || ||  ||||||| || |||||||| |||||  | || |
gtacatgtcttccttttgatgtcatgatgttatatttggggtgtttgtttgtagttagctcatta-atagtaataataatttttttgcatgaacttgttgtacaaggcatcttttat--ggtgactggttttccatctctgtagttttttaacgtttgttgcattatgttgctgcagGGAGCTTTGGATGGTGGACTGGATATTCCTCACAGCGAGAAGAGGTTTGCTGGTTTCAAGAAGGATGACAAGCAGCTGGATGCTGATATCCATCGCAAGT

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 6
gtattgtgttttaatgtggttgtctgtgttcttatctgttgtatagtgtgttcatgatttgaagatgatgctagcaatcctttaataccctgttggtttgcttcatgaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCTGGTTTCCACAAAGAGAACAAGCAACTTGATGCTGAAATCCACAGGAACT
    |     || || |  ||  |  ||  ||   || ||||   || |||| | |   | | | |  |      |    ||||| ||    |  | ||| |        ||  ||||||||||||| || ||||| ||||| |||||||| || ||||| |||||||| ||| | || ||  | ||||| || |||||||| |||||| | || |
----ttcccatttatctaatttccattgaactatacttttgtt--gtatgtttaaggaat-atgtttttatggatagcattttaacacaagat--gcttgtt-------gctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv05s0094g00870.t01 (Vitis vinifera), 3'ss of exon 6
gtattgtgttttaatgtggttgtctgtgttcttatctgttgtatagtgtgttcatgatttgaagatgatgctagcaatcctttaataccctgttggtttgcttcatgaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCTGGTTTCCACAAAGAGAACAAGCAACTTGATGCTGAAATCCACAGGAACT
             |      ||||  | |  | |  || | | |  |  ||| |   |||  |  |||  |||   || |   |       ||   ||   ||||   ||||| |||||||  |||| || ||  | || || |||||||||||||||||||||||||| |||   || || | |||||| |||||||| ||  | ||  | || |
------------tacactactgtccat-tcatgacatgct-tgtttttggttgaatgttt--acttgagtctacttattcccaagctagaggtcatttaatttcaattaactacagGGAGCACTGGATGGTGGCTTGGACATTCCTCACAGTGACAAGAGATTTGCTGGATTCTCAAAGGATAGCAAGCAGCTTGATGCCGAGGTTCATCGAAAGT

upper sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv00s0174g00190.t01 (Vitis vinifera), 3'ss of exon 6
gtattgtgttttaatgtggttgtctgtgttcttatctgttgtatagtgtgttcatgatttgaagatgatgctagcaatcctttaataccctgttggtttgcttcatgaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCTGGTTTCCACAAAGAGAACAAGCAACTTGATGCTGAAATCCACAGGAACT----
      || ||  |  || || | |   ||   || ||      | |     |||   || |   |||  ||       |   | |  ||||||  |   |||     || |  ||||||| ||||| || || |||||||| ||||||||||||||||| |||||||| |||  ||  ||    |||||||||||||||||  | ||| | || |    
---aaatgattccagatgattctttaattttgaatttgcc---cattcaaaccatctcttcatcttgagcct-------cagcagttacctgtt--tcctctt-----aattccagggagCATTGGATGGTGGACTTGATATTCCTCACAGTGACAAGAGGTTTGCTGGATTCAGCAGGGATGGTAAGCAACTTGATGCTGATGTTCACCGCAAGTATAT

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|164049117|gb|ES187432.1|ES187432
EST:     TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGT
genomic: TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGT
EST: gi|164090744|gb|ES125769.1|ES125769
EST:     CCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAAGAGATTTGC
genomic: CCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAA-GAGATTTGC
EST: gi|125017746|gb|EL090015.1|EL090015
EST:     CTACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGA
genomic: CTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGA
EST: gi|163980490|gb|ES071119.1|ES071119
EST:     GGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCT
genomic: GGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCT
EST: gi|125297938|gb|EL312023.1|EL312023
EST:     TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGG
genomic: TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGG
EST: gi|164121875|gb|ES155835.1|ES155835
EST:     TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATT
genomic: TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATT
EST: gi|116398433|gb|EG441025.1|EG441025
EST:     TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGC
genomic: TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGC
EST: gi|124707921|gb|EH799323.1|EH799323
EST:     TACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAAGGTCTTGATATCCCTCACAGTGACAA
genomic: TACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGA-GGTCTTGATATCCCTCACAGTGACAA
EST: gi|125188113|gb|EL203067.1|EL203067
EST:     TTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCT
genomic: TTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCT
EST: gi|164056865|gb|ES093947.1|ES093947
EST:     TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGTTACAAGAGATT
genomic: TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTG--ACAAGAGATT
EST: gi|116398349|gb|EG440941.1|EG440941
EST:     TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAG                         GGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCT
genomic: TTGGACTTATCAGGACTACCACTGGAAACCGTGTGTTTGGTGCACTCAAGgtattgtgtt ... gaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatgatgctagcaatcctttaataccctgttggtttgcttcatgaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCTGGTTTCCACAAAGAGAACAAGCAACTTGATGCTGAAATCCACAGGAACT
                  ctttaat  putative branch site (score: 4)
                   tttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtgttttaatgtggttgtctgtgttcttatctgttgtatagtgtgttcatgatttgaagatgatgctagcaatcctttaataccctgttggtttgcttcatgaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCTGGTTTCCACAAAGAGAACAAGCAACTTGATGCTGAAATCCACAGGAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG