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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgttttcttcttagcttcgttcattgttttgctttagctcttgtttttgaagttgatggagacagtgatgattgtgtaatgcgttggttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGTGAAGTTTATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTC

Basic information

species Arabidopsis thaliana
transcript AT2G27860.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 2
gtatgtgttttcttcttagcttcgttcattgttttgctttagctcttgtttttgaagttgatggagacagtgatgattgtgtaatgcgt-tggttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGTGAAGTTTATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTC
    ||  |  || ||   || |  ||    |||    ||     |  ||| |     |  || ||| | || |||| |    | | || || | |    |||| || ||||| ||||||||||||||||||||||| ||||| || || || || || || || || ||||| || ||||| || || |  || || ||||
----gtaatccctcctcttctccactccagatttcttctt---cttcttttctaccactagtgcaga-attgttgatgg----acgtgtgtgatgtgcacagGTCAAGTACTGCTCTGAGAACAACAAGCGTCTCATCCACTTCTCCACGTGCGAGGTCTACGGCAAGACCATCGGCAGCTTCCTCCCCACCGACCACCCTC

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 2
gtatgtgttttcttcttagcttcgttcattgttttgctttagctcttgtttttgaagttgatggagacagtgatgattgtgtaatgcgttggttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGTGAAGTTTATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTC
   || || ||  | ||| |||   |  || | |  ||||     |||||||    ||   |||| |     ||    |  |      | ||||     ||||||| |||||||| ||||||||||||||||||||||| || ||||| |||||||| ||||| ||||| ||||||||||| || || || |||  |||||
--gtgcgtcttactttta-ctttact--ttctctcccttttttctttgttttctgtgtgtttggaaattcaaattgaggattggaatttgggttc----agGTGAAGTACTGTTCAGAGAACAACAAGCGTCTCATTCATTTCTCTACGTGTGAAGTCTATGGGAAAACGATTGGAAGCTTCCTCCCCAAAGATAGTCCTC

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 2
-----gtatgtgttttcttcttagcttcgttcattgttttgctttagctcttgtttttgaagttgatggagacagtgatgattgtgtaatgcgttggttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGTGAAGTTTATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTC
      ||  |  ||   |     |    |  | |        | |  | |||  | |  | |   | |||   |    ||    ||  | ||||  ||||  ||||||||||||||||| |||||||||||||| || || || || ||||| || ||||| || ||||| || ||||||  |||||| ||||| |||  |||||
gtaacttaactacttcactaactacccgttctaattgcaaatgtgaattgttgaatcttgaatgatttgagttcgattcgacgtcgt--ttcgttcttttttgtagGTGAAATACTGTTCCGAGAACAACAAGCGCCTTATCCATTTCTCTACTTGCGAAGTGTACGGAAAGACGATTGGAGCCTTTCTCCCTAAAGATAGTCCTC

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 2
gtatgtgttttcttcttagcttcgttcattgttttgctttagctcttgtttttgaagttgatggagacagtgatgattgtgtaatgcgttggttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGTGAAGTTTATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTC
|||  |   |        | |    |      | ||    | | ||   | |||| | |  | |||        ||    ||  || | |    |||| |||||||||||||||| |||||||||||||| || || || || || || || ||||| || || ||||| ||||||  |||||| ||||| |||  |||||
gtaactaactaaccacctgttcaaattgaaaatgtga---aacgctgaatcttgagggt--ttgagttctatgcgacgtcgttttgtgct----ttgt-agGTGAAATACTGTTCCGAGAACAACAAGCGCCTTATCCATTTCTCCACTTGCGAAGTGTACGGGAAAACGATTGGAGCCTTTCTCCCTAAAGATAGTCCTC

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 2
----------------------gtatgtgttttcttcttagcttcgttcattgttttgctttagctcttgtttttgaagttgatggagacagtgatgattgtgtaatgcgttggttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGTGAAGTTTATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTC
                      | ||  |||||| ||  ||  |  |  |||||| |   ||   |  | | |  ||| |   | ||  |  |||||  || ||  ||   ||| | | |||||||||||||||||| |||||||||||||||||||||||||| || || |||||||| ||||| ||||| ||||| ||||||||||| || |||   || |
gtatgctgttggatgcttgtttgaattcgttttcgtccaaggataat--attgttgttagtttttttgtttctcggaaatctgttgaagc--tgatg--tgcgttttgatgtggctct-ttagGTGAAATACTGTTCGGAGAACAACAAGCGTCTCATTCACTTCTCGACTTGTGAAGTCTATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCCC

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 2
----------------------gtatgtgttttcttct-----tagcttcgttcattgttttgctttagctcttg---tttttgaagttgatggagacagtgatgattgtgtaatgcgttggttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGTGAAGTTTATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTC
                      | ||   ||||| |       ||   | |||  |||| ||  | |  |||       | |||||| ||||| |  |  ||||  ||| ||  ||   ||| ||| |||||||||||||||||| || ||||||||||||||||||||||| || || |||||||| ||||| ||||| ||||| ||||||||||| || |||   ||||
gtatgctgttggatgtttgtttgaattatttttcgttcaaagataatgttgttatttgtctttttgtttctcggaaatctgttgaagctgatgtatgcgttgat--ttgcgttttgatgtggcttt-ttagGTGAAATACTGTTCAGAAAACAACAAGCGTCTCATTCACTTCTCGACTTGTGAAGTCTATGGGAAAACGATTGGGAGCTTTCTTCCCAAAGATTCACCTC

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ07025 (Selaginella moellendorffii), 3'ss of exon 2
----gtatgtgttttcttcttagcttc--------gttcattgttttgctttagctcttg-------tttttgaagttgatggagacagtgatgattgtgtaatgcgttggttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGTGAAGTTTATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTC
    ||  || |||| |||||||| |         |||  | ||| |  |||||  ||||       |||||  || | ||        |  ||    |  | ||  |  |       |||| | ||| || || || |||||||||||  | || || |||||||| || ||||| ||||||||||| |||||||||||| | ||  ||||   | |  
gtaagtcggtatttt-ttcttagcgtttccagagtgtttttagttcttttttagagcttgatagttgtttttagagcttattttttgctttttggaacttaagtgactgagaacgaacagGTTAGATATTGCTCGGACAACAACAAGCGCTTGATCCATTTTTCTACGTGCGAAGTGTATGGAAAAACGATTGGAAGCTTTTTGCCCGAGGACAGTTCCT

upper sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ18978 (Selaginella moellendorffii), 3'ss of exon 2
-----------gtatgtgttttcttcttagcttcgttcattgttttgctttagctcttg-------tttttgaagttgatggagacagtgatgattgtgtaatgcgttggttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGTGAAGTTTATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTC
           || | | ||  | | |       |||  | ||| |  |||||  ||||       |||||  || | ||        |  ||    |  | ||  |  |       |||| | ||| || || || |||||||||||  | || || |||||||| || ||||| ||||||||||| |||||||||||| | ||  ||||   | |  
gtaagtcggtagtttttcttagcgtttcgagagtgtttttagttcttttttagagcttgatagttgtttttagagcttattttttgctttttggaacttaagtgactgagaacgaacagGTTAGATATTGCTCGGACAACAACAAGCGCTTGATCCATTTTTCTACGTGCGAAGTGTATGGAAAAACGATTGGAAGCTTTTTGCCCGAGGACAGTTCCT

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|116380180|gb|EG422772.1|EG422772
EST:     CACGTCCTCTTGATACTATCTACAGCAATTTCATTGATGCGCTTCCAGTT                         GTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGT
genomic: CACGTCCTCTTGATACTATCTACAGCAATTTCATTGATGCGCTTCCAGTTgtatgtgttt ... gttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGT
EST: gi|116380179|gb|EG422771.1|EG422771
EST:     CACGTCCTCTTGATACTATCTACAGCAATTTCATTGATGCGCTTCCAGTT                         GTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGT
genomic: CACGTCCTCTTGATACTATCTACAGCAATTTCATTGATGCGCTTCCAGTTgtatgtgttt ... gttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGT
EST: gi|116377085|gb|EG419677.1|EG419677
EST:     CACGTCCTCTTGATACTATCTACAGCAATTTCATTGATGCGCTTCCAGTT                         GTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGT
genomic: CACGTCCTCTTGATACTATCTACAGCAATTTCATTGATGCGCTTCCAGTTgtatgtgttt ... gttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGT
EST: gi|116377084|gb|EG419676.1|EG419676
EST:     CACGTCCTCTTGATACTATCTACAGCAATTTCATTGATGCGCTTCCAGTT                         GTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGT
genomic: CACGTCCTCTTGATACTATCTACAGCAATTTCATTGATGCGCTTCCAGTTgtatgtgttt ... gttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGT
EST: gi|116380174|gb|EG422766.1|EG422766
EST:     CACGTCCTCTTGATACTATCTACAGCAATTTCATTGATGCGCTTCCAGTT                         GTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGT
genomic: CACGTCCTCTTGATACTATCTACAGCAATTTCATTGATGCGCTTCCAGTTgtatgtgttt ... gttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGT
EST: gi|116380171|gb|EG422763.1|EG422763
EST:     CACGTCCTCTTGATACTATCTACAGCAATTTCATTGATGCGCTTCCAGTT                         GTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGT
genomic: CACGTCCTCTTGATACTATCTACAGCAATTTCATTGATGCGCTTCCAGTTgtatgtgttt ... gttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttgaagttgatggagacagtgatgattgtgtaatgcgttggttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGTGAAGTTTATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTC
         agttgat  putative branch site (score: 5)
                                              ttttgtt  putative PPT
                                              ttttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgttttcttcttagcttcgttcattgttttgctttagctcttgtttttgaagttgatggagacagtgatgattgtgtaatgcgttggttttgttagGTGAAATACTGTTCTGAGAACAACAAGCGTCTCATTCACTTTTCTACCTGTGAAGTTTATGGAAAAACCATTGGAAGCTTTCTTCCTAAGGATCATCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG