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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttagattttctctgcttcttttgtgtgttttagttgatgttgatcttttgtaatatagcattgcttgtatttgccaacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA

Basic information

species Arabidopsis thaliana
transcript AT2G45290.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 2
---------gttagttagattttctc-tgcttct---tttgtgtgttttagttgatgttgatcttt-tgtaatatagcattgcttgtatttgccaacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA
          | |  |  |  |  |    | | |   ||| | || || | |  ||   || ||   |||         ||| |||  || |      || ||| |||||||| || |||||||||||||| |||||  | || ||||| ||||||||  |||||||| | || ||||| || ||||  ||||||||||| ||
gtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttgaatacatacagaactgaatgtttcggtttcttgtttggtttcgttc---tgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA

upper sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os04g19740.1 (Oryza sativa), 3'ss of exon 2
--------gttagttagattttctctgcttcttttgtgtgttttagttgatgttgatcttttgtaatatagcattgcttgtatttgccaacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA
         ||      |||||    | ||  ||| |    ||  | || | ||         | |  || |  |       | ||     ||||||||||||| || || ||| ||||||||||||||||  |||| ||||| ||||| ||| | |||||  | || || || |||||     | || || || ||
gtttgcctcttgtactaatttttaaagtttgctttatccccttctggtgttcttccggaaaaattacctatctctaaaaccttctgatgttatgcagGTCCTCTGGGGCAGGGTTTTGCAAATGCTGTTGGCCTAGCGCTTGCTGAGAAACATCTAGCTGCCCGTTTCAATAAGCCTGATTTGAAAATCGTGGATCA

upper sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G010494_T01 (Zea mays), 3'ss of exon 2
---gttagttagattttctctgcttcttttgtgtgttttagttgatgttgatcttttgtaatatagcattgcttgtatttgccaacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA
   |  || |  |   | |    || |  | ||  || |   ||||  | |  ||     ||||     |     | | ||    |||| |||||||||||| || ||| ||||||||||||||||  |||| ||||| ||||| ||| | ||| |  | || |||||  ||||||   |  | || |||||
gttgccagctgaaacattttaaattttgctttgccttctt-ctgatacttaaatt----gatat----ctaaacttttctgatgccatgtagGTCCTCTTGGGCAGGGTTTTGCAAATGCTGTTGGACTAGCACTTGCTGAGAAACATCTAGCTTCACGTTTCAACAAGACTGACATGAAAGTCGTGGACCA

upper sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G03200.1 (Glycine max), 3'ss of exon 2
-------gttagttagattttctctgcttcttttgtgtgttttagttgatgttgatcttttgtaat-atagcattgcttgtatttgccaacat-gcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA
        | ||||||| ||| | |  |    | ||   || |  ||  | || || |||  |  | ||    ||     |  |||| |   | | |||||||||||| || || ||||| |||||||||||||| || ||||| |||||||| |||||||| ||||  ||||| |||||||||||||||||||||||
gtttgatatgagttagagtttgtataatagaatagta-attctttttattttttatttttattgtttatttatttatccattattgctatttttgtagGTCCTCTTGGTCAGGGGATTGCCAATGCTGTTGGTTTGGCCCTTGCAGAGAAGCACTTGGCTGCAAGATACAACAAGCCTGACAATGAGATTGTTGACCA

upper sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 2
gttagttagat-tttctctgcttcttttgtgtgttttagttgatgttgatcttttgtaatatagcattgcttgtatttgc-caacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA
    ||||||| ||||  || ||  | |   |||| |  | | ||  |   |||||   | |    |||||| |  |  |      |  |||||||||||| || || ||||| ||||||||||| ||||| || || |||||||| ||||||||  |||||||||| |||||||||||||||||||||||
----gttagatgtttcattggtttatgttactgttatcat-ggtga-gcctttttgctgtgttctgttgcttatcctcacgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGATTAGCACTAGCTGAGAAGCACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA

upper sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G38720.1 (Glycine max), 3'ss of exon 2
gttagttagattttctctgcttcttttgtgtgttttagttgatgttgatcttttgtaatatagcattgcttgtatttgc-caacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA
||||| ||  |||  |  | || | || | |||| |  | |     |   |||||   | |    |||||| |  | |       |  |||||||||||| || || ||||| ||||||||||| ||||| || || ||||| || ||||||||  |||||||||| |||||||||||||||||||||||
gttagata--tttcattagtttatgttat-tgttatcatagtga--gcctttttgctgtgtcctgttgcttatcctcgtgttttgtttagGTCCTCTTGGTCAGGGCATTGCCAATGCTGTTGGGTTAGCACTAGCTGAGAAACACTTGGCTGCACGATTTAACAAGCCTGACAATGAGATTGTTGACCA

upper sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0022g01440.t01 (Vitis vinifera), 3'ss of exon 2
gttagttagattttctctgcttcttttgtgtgttttagttgatgtt-gatcttttgtaatatagcattgcttgtatttgccaacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA
||| | | | | |||  ||   |||   |   | |  ||  ||||| ||    |  |||     | ||   |||  ||||     |  ||| |||||||| || |||||||| |||||||||||||| ||   || |||||||||||||||||| ||||| ||||||||||||||||||||||| |||||
gttggct-gctgttccttgaaacttaattcaatgtctgt--atgttagaatgctaataaccggtccttatgtgttattgct--tttatagGCCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGTTTGGCCGCTGTGGAGAAGCATTTGGCTGCAAGATTCAACAAACCTGACAATGAGATTGTCGACCA

upper sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 2
gttagttagatttt--ctctgcttcttttgtgtgttttagttgatg----------ttgatcttttgtaatatagcattgcttgtatttgccaacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA
    |||||||| |     ||  | ||   | ||||||  ||| ||            ||    ||||  |  | |   ||   |  || ||    || |||||||||||| || |||||||| ||||||||||| || ||||||||||||| ||| ||||||||| |||| |||||||| ||||||||||||||||| ||
----gttagattctagtcttgaatgttaaatctgttttgtttgctgaaccatacaacagaggcgttgttgttcatctgggcacatccttccctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCA

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|116467576|gb|EG510168.1|EG510168
EST:     TCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTG                         GTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGA
genomic: TCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTGgttagttaga ... caacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGA
EST: gi|116464596|gb|EG507188.1|EG507188
EST:     TCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTG                         GTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGA
genomic: TCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTGgttagttaga ... caacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGA
EST: gi|116480249|gb|EG522841.1|EG522841
EST:     CCAGGACATCCTGAGAATTTTGAGACTCCCTGGTGTTGAAGCCACTACTG                         GTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGA
genomic: CCAGGACATCCTGAGAATTTTGAGACTCC-TGGTGTTGAAGCCACTACTGgttagttaga ... caacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagttgatgttgatcttttgtaatatagcattgcttgtatttgccaacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA
        tgttgat  putative branch site (score: 4)
             atcttttgtaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttagattttctctgcttcttttgtgtgttttagttgatgttgatcttttgtaatatagcattgcttgtatttgccaacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT