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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccattctctcagcaatgaatcttacttgattgctgacagtactatatcacacaaaatcaatcttaagtatatttcttttaaagttgtttaacatatcacacagagttttgtctaggtttttcatgtttataagtgtttttttcctgttagGTCTCGTTGATCTTAAGAGGTGCAAATGACTACATGCTTGATGAGATGGAGAGAGCACTGCATGACGCTTTATGTATTGTCAAGAGGACCCTTGAGTCCA

Basic information

species Arabidopsis thaliana
transcript AT3G20050.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G039263_T01 (Zea mays), 3'ss of exon 12
gtatgccattctctcagcaatgaatcttacttgattgctgacagtactatatcacacaaaatcaatcttaagtatatttcttttaaagttgtttaacatatcacacagagttttgtctaggtttttcatgtttataagtgtttttttcctgt-tagGTCTCGTTGATCTTAAGAGGTGCAAATGACTACATGCTTGATGAGATGGAGAGAGCACTGCATGACGCTTTATGTATTGTCAAGAGGACCCTTGAGTCCA
                                                             |  |  ||    |||    ||||||    ||||    ||  |   | |  ||          ||| |||    ||| || ||||    |||  |||||||  | ||  | || || |||||||||||||||||||||||||| ||  |  |  ||||||| ||  | || ||||| ||||| ||||| || || |
----------------------------------------------------------gtttgtactttttccataccaattttaagcaagttttctgtaagaggaacaaattcaa-------ttttatg---gtaattgattttccattgtgcagGTCTCTATAATACTTAGGGGCGCAAATGACTACATGCTTGATGAGATTGAACGGTCCTTGCATGATGCCCTGTGCATTGTGAAGAGAACCCTGGAATCAA

upper sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA05G29870.1 (Glycine max), 3'ss of exon 12
gtatgccattctctcagcaatgaatcttacttgattgctgacagtactatatcacacaaaatcaatcttaagtatatttcttttaaagttgtttaacatatcacacagagttttgtctaggtttttcatgtttataagtgtttttttcctgttagGTCTCGTTGATCTTAAGAGGTGCAAATGACTACATGCTTGATGAGATGGAGAGAGCACTGCATGACGCTTTATGTATTGTCAAGAGGACCCTTGAGTCCA
                                                ||   ||  |        |     ||  ||  | || |  || | ||      ||||  | |  | ||   ||| |  | || || |  ||||| || | |||| ||||| | |||||  ||||||||||||||||| | ||||||||||||||||| ||||| |||||||| || || |  ||||||||||| || ||||| || |
-----------------------------------------------catgcaacgtatggggggacactgatagtttattattta--ttatctagtg---cacattgtggatagttgcggtatcacctgattct--gtgttgttcttctgt-agGTCACTTTGATTCTAAGAGGTGCAAATGACCATATGCTTGATGAGATGGATAGAGCTCTGCATGATGCATTGTCCATTGTCAAGAGAACTCTTGAATCAA

upper sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 12
gtatgccattctctcagcaatgaatcttacttgattgctgacagtactatatcacacaaaatcaatcttaagtatatttcttttaaagttgtttaacatatcacacagagttttgtcta-ggtttttcatgtttataagtgtttttttcctgttagGTCTCGTTGATCTTAAGAGGTGCAAATGACTACATGCTTGATGAGATGGAGAGAGCACTGCATGACGCTTTATGTATTGTCAAGAGGACCCTTGAGTCCA
                                              | ||   ||  |      |   |     | | |  ||||   || | |       ||||  |||  | |  |  ||| |  | || || |  ||||| |||||    |||||| | |||||  ||||||||||||||||| | ||||||||||||||||| ||||| |||||||| || || |  ||||||||||| || ||||| || |
----------------------------------------------ccatgcaacgtatgggggacactgctagtttattattta---ttatctggtg---cacattgaggatagcttgtggtatcacctgattct--gtgttgttttctg--tagGTCACTTTGATTCTAAGAGGTGCAAATGACCATATGCTTGATGAGATGGACAGAGCTCTGCATGATGCATTGTCAATTGTCAAGAGAACTCTTGAATCAA

upper sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 12
gtatgccattctctcagcaatgaatcttacttgattgctgacagtactatatcacacaaaatcaatcttaagtatatttcttttaaagttgtttaacatatcacacagagttttgtctaggtttttcatgtttataagtgtttttttcctgtt-agGTCTCGTTGATCTTAAGAGGTGCAAATGACTACATGCTTGATGAGATGGAGAGAGCACTGCATGACGCTTTATGTATTGTCAAGAGGACCCTTGAGTCCA
                                                  ||   | |  |  || |||    |   | || || ||  || |||   ||   ||    ||| |  |    | |    || || |   | |  | ||  |||| |||| || || ||| | |||||||| |||||||| ||||||||||||||||| || ||  ||||||| ||| |||  |||||||||||||||||||| ||||
--------------------------------------------------att-tatatcactaaccttctacaatctgctgttcaa--tggtta---tacagcatgaggttcttgcattttataatctgattcttcttatcatgttattgttcagGTTTCCTTAATCCTCAGAGGTGCTAATGACTATATGCTTGATGAGATGGATAGGGCTTTGCATGATGCTCTATCAATTGTCAAGAGGACCCTTGAATCCA

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|164194911|gb|ES208295.1|ES208295
EST:     TATTGATAAAGGGAACCAAAACAAGTAGTGCG                         GTCTCGTTGATCTTAAGAGGTGCAAATGACTACATGCTTGATGAGATGGAG
genomic: TATTGATAAAGGGAACCAAAACAAGTAGTGCGgtatgccatt ... ttcctgttagGTCTCGTTGATCTTAAGAGGTGCAAATGACTACATGCTTGATGAGATGGAG
EST: gi|164014412|gb|ES057230.1|ES057230
EST:     GATGATGATGTTATATTGATAAAGGGAACCAAAACAAGTAGTGCG                         GTCTCGTTGATCTTAAGAGGTGCAAATGACTACATGCTTGATGAGATGGA
genomic: GATGATGATGTTATATTGATAAAGGGAACCAAAACAAGTAGTGCGgtatgccatt ... ttcctgttagGTCTCGTTGATCTTAAGAGGTGCAAATGACTACATGCTTGATGAGATGGA
EST: gi|125197275|gb|EL212229.1|EL212229
EST:     TCGCAGATGATGATGTTATATTGATAAAGGGAACCAAAACAAGTAGTGCG                         GTCTCGTTGATCTTAAGA
genomic: TCGCAGATGATGATGTTATATTGATAAAGGGAACCAAAACAAGTAGTGCGgtatgccatt ... ttcctgttagGTCTCGTTGATCTTAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacacagagttttgtctaggtttttcatgtttataagtgtttttttcctgttagGTCTCGTTGATCTTAAGAGGTGCAAATGACTACATGCTTGATGAGATGGAGAGAGCACTGCATGACGCTTTATGTATTGTCAAGAGGACCCTTGAGTCCA
                                      tgtttttttcctgtt  CT-rich tract
                              tttataagtgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccattctctcagcaatgaatcttacttgattgctgacagtactatatcacacaaaatcaatcttaagtatatttcttttaaagttgtttaacatatcacacagagttttgtctaggtttttcatgtttataagtgtttttttcctgttagGTCTCGTTGATCTTAAGAGGTGCAAATGACTACATGCTTGATGAGATGGAGAGAGCACTGCATGACGCTTTATGTATTGTCAAGAGGACCCTTGAGTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA