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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctctgctcgtctttttcttcttctttcccttgattttgctgattgttgttttagtttacgggatggtatcatagttgttcataggtaggattttagatgttttcttctctgttgttaaaatagatttcttatatctttctaacatttggcagATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAG

Basic information

species Arabidopsis thaliana
transcript AT3G04500.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G068255_T01 (Zea mays), 3'ss of exon 1
gtaagctctgctcgtctttttcttcttctttcccttgattttgctgattgttgttttagtttacgggatggta-tcatagttgttcataggtaggattttagatgtttt---cttctctgttgttaaaatagatttcttatatctttctaacatttggcagATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAG
                                                                    | | |  ||   |     ||   |    |||    ||||||   ||||||  || ||  | |   ||   | |    |  ||||| || ||||| ||||| || ||||||||||| ||||| || |||||||| |||||||||||||| |||||||||||| |  | || ||  ||||||| ||||| | |
-------------------------------------------------------------------gtagcagccaacataacctattaatccagtttcctttgttttatgcttctcccttatttcatttccttgtgtttcaactcttaacaatttgcagACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGG

upper sequence: AT3G04500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G016106_T01 (Zea mays), 3'ss of exon 1
gtaagctctgctcgtctttttcttcttctttcccttgattttgctgattgttgttttagtttacgggatggtatcatagttgttcataggtaggattttagatgttttct---tctctgttgttaaaatagatttcttatatctttctaacatttggcagATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAG
                                                                  |  | || ||||  |  | | |   ||  |  |   |||||  |   || |  || ||    | | ||   | |    | |||||| || ||||| ||||| || ||||||||||| ||||| || |||||||| |||||||||||||| |||||||||||  |  | || ||  ||||||| ||||| | |
------------------------------------------------------------------gtagctaacataacttatta-attcagtttcctttgtgtttaatggatcacccttatttggtttgcttgtgtctcaactcctaacaatttgcagACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTATCCAAAGCATTCTCACGGTTTCCATCCTTCAACATGGCAAGG

upper sequence: AT3G04500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G36570.1 (Glycine max), 3'ss of exon 2
gtaagctctgctcgtctttttcttcttctttcccttgattttgctgattgttgttttagtttacgggatggtatcatagttgttcataggtaggattttagatgttttcttctctgttgttaaaatagatttcttatatctttctaacatttggcagATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAG
                                                       | ||  ||    |||| ||      |  | ||    | ||||||  | |||   |      | || ||   |  |||||| | |  |  |     ||   |||||| ||||| || |||||||| |||||||| ||||| ||||||||||||||||| || ||||||||| |  | || ||  |||| ||  ||||    
-----------------------------------------------------cctgagcctat---atggaatttgtaatcatgattttgaagattttgaa-gttagataagaaatcgtgaattgatttttctttttttctattttggattattagATGATTATCGGCTCTTCTGTGGGGATCTTGGTAACGAGGTGAATGATGATGTTCTCTCAAAAGCATTTTCACGGTTTCCTTCCTTTAACTTGGCACGA

upper sequence: AT3G04500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G30900.2 (Glycine max), 3'ss of exon 2
gtaagctctgctcgtctttttcttcttctttcccttgattttgctgattgttgttttagtttacgggatggtatcatagttgttcataggtaggattttagatgttttcttctctgttgttaaaatagatttcttatatctttctaacatttggcagATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAG
                                            ||  |||   |||||| ||    |||| ||      || |  |   |  ||  ||||||  ||  |  |   ||| |    ||  ||| ||  || |||  |  |||    |||||| ||||| || |||||||| |||||||| ||||| ||||||||||||||||| || ||||||||| |  |||| ||  |||| || |||||    
--------------------------------------------tgtatgtgtgtttagtctat---atggaatttg---tgattgtgattttgaagttagataattaatcatgaattgatt---tatctttttttcatttttggatgatt----agATGATTATCGGCTCTTCTGTGGGGATCTTGGTAACGAGGTGAATGATGATGTTCTCTCAAAAGCATTTTCACGATTTCCTTCCTTTAACATGGCACGA

upper sequence: AT3G04500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G01300.1 (Glycine max), 3'ss of exon 2
gtaagctctgctcgtctttttcttcttctttcccttgattttgctgattgttgttttagtttacgggatggtatcatagttgttcataggtaggattttagatgttttct-tctctgttgttaaaatagatttcttat-atctttctaacatttggcagATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAG
                                                   ||||||  ||  | |||   |||     ||||  ||  |    |||||| |  || |   | |   ||   |   |  |||  || | || |||||  |  |    |||||| ||||| || || || || |||||||| || ||||||||||||||||||||||| |||| |||| |  |||||||  |||| ||  ||||   |
-------------------------------------------------agtgttttgtttgcctggagcctat----attgtgtatgtg----attttaaagattctgaatttagattagaatcgtgaattgattgttatttttctggc--taattagATGATTATCGGCTCTTTTGCGGCGATCTTGGTAATGAAGTGAATGATGATGTTCTTTCAAAAGTATTTTCACGATTCCCTTCCTTTAACTTGGCACGG

upper sequence: AT3G04500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0036g00630.t01 (Vitis vinifera), 3'ss of exon 2
gtaagctctgctcgtctttttcttcttctttcccttgattttgctgattgttgttttagtttacgggatggtatcatagttgttcataggtaggattttagatgttttcttctctgttgttaaaatagatttcttatatctttctaacatttggcagATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAG
                                       ||   |||   |  |  ||   | | | ||    || ||    | | |   |  |  |  | ||| ||   ||     ||  | ||  |                |  |||   |||||||| |||||| | || |||||||||||||| || || |||||||||||||||||||| ||||||||| |  |||| ||  ||||||||||||| || 
---------------------------------------ttcattgacattattcctatgatgctgtatatgttcctacccctcctt---tttgcctggatatgcttctctcatgcctggcagaactg---------------ttggcatcctgcagATGATTATCGTTTATTTTGTGGTGATCTTGGCAATGAGGTGAATGATGATGTTCTTTCAAAAGCATTTTCACGATTTCCTTCCTTCAATATGGCTAAA

upper sequence: AT3G04500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0018g01710.t01 (Vitis vinifera), 3'ss of exon 2
gtaagctctgctcgtctttttcttcttctttcccttgattttgctgattgttgttttagtttacgg-gatggtatcatagttgttcataggtaggattttagatgttttcttctctgttgttaaaatagatttcttatatctttctaacatttggcagATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAG
                                                       ||  || ||   | |  ||| || | | || || | |   |  |    | ||| | |   | |  ||     |   ||   | | || | |  ||||  |||||||| |||||| | || |||||||||||||| || || ||||| |||||||||||||| ||||||||| |  |||| ||  |||||||||||||||  
-------------------------------------------------------ttcattcacactgtttctatgat-gctatttat-gttcctacctctcctttttgcctggatatgcttctctcatgcttggaagaactgt-tggcattctgcagATGATTATCGTTTATTTTGTGGTGATCTTGGCAATGAGGTGAACGATGATGTTCTTTCAAAAGCATTTTCACGATTTCCTTCCTTCAATATGGCCAGA

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|116430691|gb|EG473283.1|EG473283
EST:     AGCTGCGGGACAGTCTTGGGAGGATCCTACTCTTTCAGAATGGCCTGAAA                         ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATG
genomic: AGCTGCTGGACAGTCTTGGGAGGATCCTACTCTTTCAGAATGGCCAGAAAgtaagctctg ... catttggcagATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATG
EST: gi|19878344|gb|AU239175.1|AU239175
EST:     AGCTGCTGGACAGTCTTGGGAGGATCCTACTCTTTCAGAATGGCCAGAAA                         ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATG
genomic: AGCTGCTGGACAGTCTTGGGAGGATCCTACTCTTTCAGAATGGCCAGAAAgtaagctctg ... catttggcagATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATG
EST: gi|86088425|gb|DR384184.1|DR384184
EST:     AGCTGCTGGACAGTCTTGGGAGGATCCTACTCTTTCAGAATGGCCAGAAA                         ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATG
genomic: AGCTGCTGGACAGTCTTGGGAGGATCCTACTCTTTCAGAATGGCCAGAAAgtaagctctg ... catttggcagATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATG
EST: gi|47828762|gb|CK118446.1|CK118446
EST:     AGCTGCTGGACAGTCTTGGGAGGATCCTACTCTTTCAGAATGGCCAGAAA                         ATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATG
genomic: AGCTGCTGGACAGTCTTGGGAGGATCCTACTCTTTCAGAATGGCCAGAAAgtaagctctg ... catttggcagATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttcttctctgttgttaaaatagatttcttatatctttctaacatttggcagATGACTATCGTCTGTTCTGTGGTGATCTTGGGAACGAAGTGAATGATGATGTTCTTTCCAAAGCATTTGCTAGATTCCCCACCTTCAATATGGCCAAG
                                       ttctaac  putative branch site (score: 1)
                 ttaaaatagatttctt  TA-rich tract