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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccttttattgctatacggatttatttgttagttgttactcctacataactgaaaccaaacatatatttgatgtttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT

Basic information

species Arabidopsis thaliana
transcript AT4G02480.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 21
gtaccttttattgct-atacggatttatttgttagttg-----ttactcctacataactgaaacc---aaacatatatttgat------gtttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT
 ||  ||||    |  ||   |  |||| |||| | |      ||    |||  ||| |   | |   |||  |   | || |      |||   ||||||||   || || ||| || |||||||||||||||||||||| || || ||||| || || |||||||||||||| || || || || ||||| || || |
ctatattttgggacggatggagtattatatgttggctacctaattttctctatttaagtcctatcttaaaaattgcctctggtaaatctgttacttgcagCCTTGCAAGGGAATATTGCTGTTTGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATAT

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 21
----gtaccttttattgctatacggatttatttgttagt----tgttactcctacataactgaaac-caaacatatatttgat----gtttaat--gcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT
     | |   ||||     |  |  ||| ||  || ||    |||| ||  |    |  ||   | ||||||||  | ||||     |||| |   |||||    || || ||| || | ||||| || |||||||| || ||||| ||||| || ||||| || ||||| ||||||||||| ||||| ||||| || |
tagcatgctaattatcatggtctgttttttttatttggtctcttgtttcttttttccacttgtttcacaaacatagttctgatcaccatttattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 6
gtaccttttatt-------gctatacggatttatttgttagttgt-tactcctac-ataactgaaaccaaaca--tatatttgatgtttaat----gcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT
|||   ||   |       | | ||    || || |||   || | |   ||||| |||    | | |  | |  |   |  |   || | |    |||||||   || || ||| || | || ||||||||||| |||||||| || ||||| || ||||||||||||||||| || ||||| |||||||||||||| |
gtaatcttagatatgtcgagttttaaaacttcatctgtagattttcttgacctactatagtcaagatcttataactgcctccgcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G435582_T01 (Zea mays), 3'ss of exon 1
-------gtaccttttattgctatacggatttatttgttagttgt-tactcctac-ataactgaaacc----aaacatatatttgat--gtttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT
         |  | | |  | | ||    || || |||   || | |   ||||| ||     | | |    ||     |  |  ||   ||   ||||||||   || || ||| || | || ||||||||||| |||||||| || ||||| || ||||||||||||||||| || ||||| |||||||||||||| |
taatcttagatatgtcagagttttaaaacttcatctgtagattttcttgacctactatggtcaagatcttataactgcctcctcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 12
---gtaccttt-tattgctatacggatt---tatttgttagttgttactcctacataactgaaaccaaacatatatttgatgtttaat---------gcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT
   |||  ||  || || || |    ||     ||||  |  | | | |  || || | |   |   |  ||     ||||    |||         |||||||   || || ||| || | || ||||||||||| ||||| || || ||||| || ||||||||||||||||| || || || |||||||||||||| |
tttgtatattagtagtgttagatatgttgggcgtttgaaaact-tcaattgtagattattttgatgtactatggtcatgatccccaatttattctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
------gtac-cttttattgctatacggatttatttgttagttgttactcctacataactgaaaccaaacatatat--ttgatgtttaatgc------agCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT
       ||  ||| | ||   || |  |  ||    |         ||  ||  | || |||| | ||| ||| |  || || ||  || |      ||||    ||||| ||  |  | ||||| || ||||||||||||||||| ||||| || || || || |||||||||||||| || |||||||| || || |
atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G170037_T01 (Zea mays), 3'ss of exon 3
-------gtaccttttattgctatacggatttatttgttagttgt-tactcctac-ataactgaaacc----aaacatatatttgat--gtttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT
         |  | | |  | | ||    || || |||   || | |   ||||| ||     | | |    ||     |  |  ||   ||   ||||||||   || || ||| || | || ||| ||||||| |||||||| || ||||| || ||||||||||||||| | |  ||||| |||||||||||||| |
taatcttagatatgtcagagttttaaaacttcatctgtagattttcttgacctactatggtcaagatcttataactgcctcctcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATAT

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 17
------------------gtaccttttattgctatacggatttatttgtt-agttgttactcctacataactgaaaccaaacatatatttgatgtttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT
                       ||| | ||   |  | |   | ||||| ||| | |  | | |  |   |   ||| ||  | || ||  | ||   |  |||||   ||||| ||| || | ||||| |||||||| || ||||| || ||||| ||||| || ||||||||||| ||||| |||||||| || || || |
gtgaaagattttcattttagttgtttaaatgacttgtgaaagaaattgttgagtagatcatgccatgtgtgtagcacctaat-tgtaattact-ttgggtatagCCTTGCAAAGGAATATTGCTTTTTGGCCCTCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 16
--------------------gtaccttttattgctatacggat----ttatttgttagttgttactccta-cataactgaaaccaaacatatatttgatgtttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT
                    ||  |||| | ||   |  |||     || |||  ||| |  || ||  | |||   || | |    |||     | |  ||  ||  |||||   || || ||| || | ||||| || ||||| || ||||| || ||||| ||||| || ||||||||||| ||||| ||||||||||| || || |
gttgatagattttctttttagttgctttaaatgacttgtggaacacattttttagtagatcatattcgaatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
--------------------gtaccttttattgctatacggat----ttatttgttagttgttactccta-cataactgaaaccaaacatatatttgatgtttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT
                    ||  |||| | ||  |   |||     || |||  ||| || || || || |||   || | |    |||     | |  ||  ||  |||||   || || ||| || | ||||| || ||||| || ||||| || ||||| ||||| || ||||||||||| ||||| ||||||||||| || || |
gttggtagattttctttttagttgctttaaatgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
-----------------------------------------------------------------gtaccttttattgctatacggatttatttgttagttgttac---tcctacataactgaaaccaaacatatatttgatgtttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT
                                                                 | |  || | |||   || |||  ||  | |||  |  | |    | |  ||  ||   | |  | ||    ||  | |||  | ||||||   || || || ||  | ||||| |||||||| |||||||| || ||||| || || || || ||||||||||| || |||||||| ||||| || |
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatctga-atgaggttactattt--ttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
gtaccttttattgctatacggatttatttgttagttgttactcctacataactgaaaccaaacatatatttgatgtttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT
                      | | ||||||| ||| |  |  |   |  || |   | ||  |||||            |||||||   |  ||  |||| || ||||| ||||| || ||||| ||||| ||||| || || || || || || |||||||| ||||||||||||||||| |
-----------------gtctgtgtgtttgttatttgctttttttctttgtctaa---cgaatttatat-----------ggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 10
gtaccttttattgctatacggatttatttgttagttgttactcctacataactgaaaccaaacatatatttgatgtttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT
                      | | ||||||| ||| |  |  |   |  || |   | ||  |||||            |||||||   |  ||  |||| || ||||| ||||| || ||||| ||||| ||||| || || || || || || |||||||| ||||||||||||||||| |
-----------------gtctgtgtgtttgttatttgctttttttctttgtctaa---cgaatctatat-----------ggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

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|86063354|gb|DR359111.1|DR359111
EST:     TGCTTCCTCTTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAG                         CCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATG
genomic: TGCTTCCTCTTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAGgtacctttta ... tttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATG
EST: gi|124706256|gb|EH797658.1|EH797658
EST:     TTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAG                         CCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATG
genomic: TTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAGgtacctttta ... tttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagttgttactcctacataactgaaaccaaacatatatttgatgtttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT
                             aaacatatatttgatg  TA-rich tract