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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaacacctttcaatgctaagttatgcagtgtttttacatgtttctaagtaattcctacctccaaaaagagcttatgctaagtaagtttatcatctttccctctaaatatgtagACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTAGGAAAGACGAAATCATGAAGGCCATAGGGAAGAAACTGGATCGCTACAG

Basic information

species Arabidopsis thaliana
transcript AT3G06400.3
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 21
----gtaagtaacacctttcaatgc---taagttatgcagtgtt------tttacatgtttctaagtaattcctacctccaaaaagagcttatgctaagt---------aagtttatc-----atctttccctctaaatatgt----agACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTAGGAAAGACGAAATCATGAAGGCCATAGGGAAGAAACTGGATCGCTACAG
    | ||||    |  || | |     | | | ||  | ||||      |  | |  | |  |   ||   |||  | |  |    |   ||| | |||         ||| ||||      ||| ||     | | | |      ||| ||||||||||| || ||||| ||||| ||||||||||| ||||| ||  |||| || ||||| ||||  ||||| ||||||||  | || ||||| | 
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgatcattattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 21
gtaagtaacacctttcaatgctaagttatgcagtgtttttacatgtttctaagtaattcctacctccaaaaagagcttatgctaagtaagtttatcatctttccctctaaatatgtagACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTAGGAAAGACGAAATCATGAAGGCCATAGGGAAGAAACTGGATCGCTACAG
                      | | | ||  |  ||  |   |  |   || || || ||   |  ||          | ||   ||| |    ||| |||   ||    | || ||| ||||| ||||| ||||| |||||||| ||||| |||||||| || ||| ||||||| || ||||||||||| || || |||||  |||| ||||||| 
------------------gataaggctttgttgctttaattttttctggaaattagtttctgtttagaatgtttcaaggttctgcctaattggtgcattttttaatcattgtctgcagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAGGCTATTGGAAAGAAGTTGGACCGCTACAA

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 21
gtaagtaacacctttcaatgctaagttatgcagtgtttttacatgtttctaagtaattcctacctccaaaaagagcttatgctaagtaagtttatcatctttccctctaaatatgtagACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTAGGAAAGACGAAATCATGAAGGCCATAGGGAAGAAACTGGATCGCTACAG
            ||  |||   |||   |    ||| | |  || || | || |   |   |     | | | ||  | ||     |  || ||    ||||   |     | |||||| ||||||||||| ||||| |||||||| || || |||||||| || ||  ||||||| || |||||||| || || ||||||||  |||| ||||||||
------------ttaaaatatcaagg-gtttgatgtgtgttgat-ttgccaaatggcttgaattaaaatataaagggtctgtctgatttgtgta----ctttggtttatggtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
gtaagtaacacctttcaatgctaagttatgcagtgtttttacatgtttctaagtaattcctacctccaaaaagagcttatgctaagtaagtttatcatctttccctctaaatatgtagACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTAGGAAAGACGAAATCATGAAGGCCATAGGGAAGAAACTGGATCGCTACAG
                     | |  | ||  |  ||   | |||   ||      |   |  |    || | | |    |         ||| |   ||||   |     | || ||| ||||||||||| ||||| |||||||| || || |||||||| || ||  ||||||| || |||||||| || || ||||||||  |||| ||||||| 
------------------gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtctgtctgatttgtgtactttgatttatggtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 21
gtaagtaacacctttcaatgctaagttatgcagtgt-ttttacatgtttctaagtaattcctacctccaaaaagagcttatgctaagtaagtttatcatctttccctctaaata-tgtagACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTAGGAAAGACGAAATCATGAAGGCCATAGGGAAGAAACTGGATCGCTACAG
                  || ||  || |    ||  | |||||    || |  |  ||   | |    ||||  |    |  |  ||  | || | | | ||   |  || |  |  ||| |||||||| ||||| ||||||||||| || |||||||| || || ||||||||||| || |||||||| || || ||||||||  |||||||||||| 
---------------ggttgatatattgtcagatgcatcttaca-acatccatttgtttttcatc----aaaatggtgattttttcgtctgcttttaaccattaaatacaatttctccagATTATGATAGGATCATCAAGAACATTGAAAGAGGAGAGGCTAGAATTTCTAGGAAAGATGAGATCATGAAAGCAATTGGGAAGAAGTTGGATCGCTACAA

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|116481379|gb|EG523971.1|EG523971
EST:     AGTTGAAAGATATGCCAAAGTATTTAAAGAGCGGTACAAGGAGCTGAACG                         ACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTA
genomic: AGTTGAAAGATATGCCAAAGTATTTAAAGAGCGGTACAAGGAGCTGAACGgtaagtaaca ... aaatatgtagACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTA
EST: gi|116436611|gb|EG479203.1|EG479203
EST:     AGTTGAAAGATATGCCAAAGTATTTAAAGAGCGGTACAAGGAGCTGAACG                         ACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTA
genomic: AGTTGAAAGATATGCCAAAGTATTTAAAGAGCGGTACAAGGAGCTGAACGgtaagtaaca ... aaatatgtagACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccaaaaagagcttatgctaagtaagtttatcatctttccctctaaatatgtagACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTAGGAAAGACGAAATCATGAAGGCCATAGGGAAGAAACTGGATCGCTACAG
                                         ctctaaa  putative branch site (score: 3)
                               tcatctttccctcta  CT-rich tract
                                            taaatatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaacacctttcaatgctaagttatgcagtgtttttacatgtttctaagtaattcctacctccaaaaagagcttatgctaagtaagtttatcatctttccctctaaatatgtagACTATGATAGAATCATTAAGAACATTGAGAGGGGAGAGGCAAGGATCTCTAGGAAAGACGAAATCATGAAGGCCATAGGGAAGAAACTGGATCGCTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA