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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatatatatatgcatgtcactttcgaacttctttctaatcatacaattgcttacttctctacctaaacaacattcatggaaaagaagctaacacggtgcacaactgctctatgacctccagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCG

Basic information

species Arabidopsis thaliana
transcript AT2G30980.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 9
-----------------------------------gtaatatatatatatgcatgtcactttcgaacttctttctaatca-----tacaat-tgcttacttctctacctaaacaacattcatggaaaaga--agctaacacggtgcacaactgctctatgacctccagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCG
                                    ||  || | ||  |||| | || | | |  |  |||   || ||     | ||   || ||| ||    |   ||| ||  |   || |   |   | || |  |             ||  | ||| |||| ||||||||||| | |||||||| |||||||| |||||||| || || ||||| ||||| |||||||||||||| |||||||| 
gtagccatgttttcttatattggatcaccttcctcataccattt-tacttgcagggcattgtagg-ccacttcaaaaccagtttctgcatcatgtttaatttgaaataaaaaaaatgtatctgcagctgcttaactgatccatctgttgttctttcgcttaccaccagATTTTCCACAAGAGAATGCCTCCAGAAGCCATAGACCTTGCTTCCCGTCTTCTCCAATATTCACCAAGTCTACGCTGCACTGCT

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 3'ss of exon 9
------------------------------------------------------gtaatatatatatatgcatgtcactttcgaacttctttctaatcatacaattgcttacttctc-tacctaaacaac---attcatggaaaagaagcta-acacggtgcacaactgctctatgacctcc--agGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCG
                                                       |  |  | |  |||| |  |       |  ||  |||| ||| |||  |||    ||  |   || ||  ||||    ||  ||  | ||| || |  | || |      | |  ||||    || |  |||||||||||||| |||||||||| ||||| || ||||| || || || ||||||||||| ||||| ||||| || |||||||| 
gtaagcatacaatcttatccatgttgagtcatatatcacgtcatcttttatagtttcctggacaactatgaaaat-gtagctgggctcatttccaataata-gattctggacaccagatagctttacaatgcaatgtataaataaggaggtgcatacaggtactgatttttctaacttctgcgtagGTTTTCCACAAGAGGATGCCTCCTGAAGCAATAGACCTCGCTTCACGCCTTCTTCAATATTCACCGAGTCTCCGCTGCACTGCT

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G472625_T01 (Zea mays), 3'ss of exon 9
gtaatatatatatatgcatgtcactttcgaacttctttctaatcatacaattgcttacttctctacctaaacaacattcatggaaaagaagctaacacggtgcacaactgctctatgacctccagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCG
                 | | | |||    |  |  ||     || |   | ||  |  | |   |  | |   |||   |     |     |    |  |      | | | |||  ||||||| ||||||||||| | |||||||||||||||||||||||||| || || || ||||| || || |||||||| || ||| |||| 
----------------aagggcgcttaaagaaattgtttg---cagatcttagcgaaaatttgagctcagaatgcatcagttactgactgattgttccacttt----ccgttttat--cctccagATTTTCCACAAGAGAATGCCTCCGGAAGCCATTGACCTTGCTTCCCGTCTCCTTCAGTATTCGCCAAGTCTTCGCTGCTCTGCT

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 9
-------------------------------------------------------------gtaatatatatatatgcatgtcactttcgaacttctttctaa-------tcatacaattgcttacttctc-tacctaaacaacattcatggaaaaga--agctaaca--cggtgca-caactgctc--tatgacctccagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCG
                                                             ||| | | ||||  || |   |||  || ||  | |||  ||       | |   | ||| || |   || || | ||||      |   |||   |  |  ||  |   | |||  | |||   |  | |  ||||||| ||||||||||| | |||||||| |||||||| |||||||| ||||| || ||||| || ||||||||||| || ||| |||| 
gtattcatatgttaaatcatgtttctgttcacatctattatccattttacctgcaggtactgtagt-tgtatacttgtagtccacagtccaaaatgttttcaaagggcgctgaagaacttgtttgcagatcatatcgaaactttgagctcagaatgcatcaattactaactgatgcctctactttccgttttatcctccagATTTTCCACAAGAGAATGCCTCCTGAAGCCATAGACCTTGCTTCTCGTCTCCTTCAGTATTCACCAAGTCTTCGCTGCTCTGCT

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 9
gtaatatatatatatgcatgtcactttcgaacttctttctaatcatacaattgcttacttctctacctaaacaacattcatggaaaagaagctaacacggtgcacaactgctctatgacctccagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCG
                 |||| || | | | ||     ||| | |   ||  ||| | || |     | |  |  | |||| |   ||    | |  |  |  |    |   || |    | ||||||||||||||||| |||||||| ||||| ||||||||||||||  ||||||| ||||| ||||| |||||||| |||||||||
----------------gatgtaacctactacctcac--ctagtgaagtaaa-gctcagttgt-----tgattattagtcattggctagtgaatgatgcatt-tatttttatgctttatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCG

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 9
gtaatatatatatatgcatgtcactttcgaacttctttctaatcatacaattgcttacttctctacctaaacaacattcatggaaaagaagctaacacggtgcacaactgctctatgacctccagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCG----------------
           ||  |||||  |   | ||            | ||  ||     ||| || |||     | ||       |  |  |||     ||   |       |||||||||   | ||||||||||||||||| |||||||| ||||| ||||||||||||||  ||||||| ||||| ||||| ||||| || |||||||||                
-----------atgagcatgatagcattgat-----------tgatgtaacctactacctcactaataggataaagcattggctagtgaattatgcatt-tattttggtgctctatg--tttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTCCGCTGCACTGCGGTGAGTAGGATGAACT

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G15470.1 (Glycine max), 3'ss of exon 9
gtaatatatatatatgcatgtcactttcgaacttctttctaatcatacaattgcttacttctctacctaaacaacattcatggaaaagaagctaacacggtgcacaactgctctatgacctccagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCG
           ||  |||||  |   | ||            | ||  ||     ||| || |||     | ||       |  |  |||     ||   |       |||||||||   | ||||||||||||||||| |||||||| ||||| ||||||||||||||  ||||||| ||||| ||||| ||||| || |||||||||
-----------atgagcatgatagcattgat-----------tgatgtaacctactacctcactaataggataaagcattggctagtgaattatgcatt-tattttggtgctctatg--tttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTCCGCTGCACTGCG

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 8
gtaatatatatatatgcatgtcactt--tcgaacttctttctaatcatacaattgcttacttctctacctaaacaacattcatggaaaagaagctaacacggt--gcacaactgctctatgacctccagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCG
    ||  |   | | | ||||||||  |    ||| | | |||| | |    | |  |   || | | |        ||   ||    |   || |  |  |  |  |||| | || |||   | |||||||| |||||||| |||||||| ||||| ||||||||||||||  ||||||| ||||| || ||||  || |||| || ||| 
---gtaactgcgttt-cttgtcacttctttttgcttttgtttaataacagttcttccgagagcttttctt--------ttgggggggcgggcactgatgcatttggtgcaac-gatccatgg--ttcagGTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCCCCAAAACTTCGTTACAGTGCA

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 9
gtaatatatatatatgcatgtcactttcgaacttc-tttctaatcatacaattgcttacttctctacctaaacaacattcatggaaaagaagctaacacggtgcacaactgctctatgacctccagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCG
                             |||| | || ||  |||  |  ||  |  ||| | |     ||||||  |  |    | | | ||     ||||||     | || |||   | |||||||| |||||||| |||||||| ||||| ||||||||||||||  ||||||| ||||| || ||||  || |||| || ||| 
---------------------------gtaactgcgttccttgtcactccttt--tggcttttgttttataacaacgcttctactgatgcatct-----ggtgcaa---cgatccatgg--ttcagGTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCCCCAAAACTTCGTTACAGTGCA

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 9
gtaatatatatatatgcatgtcactttcgaacttctttctaatcatacaattgcttacttctctacctaaacaacattcatggaaaagaagctaacacggtgcacaactgctctatgacct---ccagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCG
                   |  |  || | |  ||| |  |   ||| |  |  ||  || ||        |   |||| || |   |  ||    |   |  | || |    ||  |  |     |||| || ||||| ||||||||||| |||||  |||| ||||| || || ||||||||||| ||||| || || || |||||||| 
-------------------ggtatgtttgtatatctgtaaaggaatatatatattttattttc--------ctgtattcttgtagttggtgcccctatt-taaaaaaataaaataaaatttgttttagGTGTTTCACAAACGGATGCCTCCTGAAGCTCTTGATCTTGCTTCACGACTTCTTCAATATTCACCGAGCCTTCGCTGCACTGCT

upper sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 10
gtaatatatatatatgcatgtcactttcgaacttctttctaatcatacaattgcttacttctctacctaaacaacattcatggaaaagaagctaacacggtg-cacaactgctctatgacctc--cagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCG
                                                                     || | || ||||     | |  ||  | |  || | |   || | |    | |   |||||||||||||||||||||||||| |||||  | ||| | |  ||  |||| ||||| || || || || || || |||| ||| 
-------------------------------------------------------------------gtaagagcaatcatccggtatat-ctctctctctgtctctcttgatgtggctcgttgacagGTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC

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|86079984|gb|DR375741.1|DR375741
EST:     ACTACACAGACTTCAGATTCCCACAAATCAAAGCCCACCCTTGGCATAAG                         GTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTT
genomic: ACTACACAGACTTCAGATTCCCACAAATCAAAGCCCACCCTTGGCATAAGgtaatatata ... tgacctccagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTT
EST: gi|124995183|gb|EL067452.1|EL067452
EST:     CAGATTCCCACAAATCAAAGCCCACCCTTGGCATAAG                         GTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTT
genomic: CAGATTCCCACAAATCAAAGCCCACCCTTGGCATAAGgtaatatata ... tgacctccagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaacattcatggaaaagaagctaacacggtgcacaactgctctatgacctccagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCG
                   agctaac  putative branch site (score: 2)
                                                cctcc  putative PPT
             aaaagaa  TA-rich tract