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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctttgtttccactcatgtcaaataaaaggctagtctcgagtttgcatgatcttttataaactctttgtagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC

Basic information

species Arabidopsis thaliana
transcript AT2G47850.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G47850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
--gtaagctttgtttccactcat-gtcaaataaaaggctagtct---cgagtttgcat----gatcttt-tataaactctttgtagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC
  || |  | | |    |   || |   | | | |  || || |   |   |||| |     ||| ||  || |||     || ||||||| || || |||||||||||  ||||||| |||||||| |||||||| |  || |||||||| ||||||||  |    | ||||  | |  |  | |
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC

upper sequence: AT2G47850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
--gtaagc-tttgtttccactcatgtcaaataaaaggctagtctcgagtttgcatgatctttt---ataaactctttgtagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC
   | ||  ||    |    |  |||    |  |    |    |    || | |  |    ||   || ||     || ||||||| || ||||||||||||||| |||| || ||||||||||| ||||||   || |||||||||||||||||  |   || ||||| | | ||  | |
gtatgagaattctcctatgattgtgtttcttggattttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC

upper sequence: AT2G47850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
----gtaagctttgtttccactcatgtcaaataaaaggctagtctcgagttt---gcatgatcttttataaactctttgtagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC
    |  |  | |  |     |    |    |  ||   |  |  |   |||   | |  |  ||  || ||     || ||||||| || ||||||||||||||| |||| || ||||||||||| ||||||   || |||||||||||||||||  |   || ||||| | | ||  | |
gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC

upper sequence: AT2G47850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G086994_T03 (Zea mays), 3'ss of exon 4
----gtaagctttgtttccactcatgtcaaataaaaggctagtctcgagttt---gcatgatcttttataaactctttgtagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC
    |  |  | |  |     |    |    |  ||   |  |  |   |||   | |  |  ||  || ||     || ||||||| || ||||||||||||||| |||| || ||||||||||| ||||||   || |||||||||||||||||  |   || ||||| | |        
gtatgagaattctcctatggatgtgcttctttgtaacatttttaactgtttttgggaaaaaatttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCG-------

upper sequence: AT2G47850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G17260.2 (Glycine max), 3'ss of exon 4
--------------------gtaagctttgtttccactcatgtcaaataaaaggctagtctcgagtttgcatgatcttttataaactctttgtagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC
                    ||     || ||    ||| ||| |   | |      |   | |  ||  |  ||   || |    | |    ||||||| || ||||||||||||||||||||||||||||| ||||||||||||||| | |||||||| ||||||||||| || ||||| ||  |  | ||| 
gtatgataatgacacttcttgttgctcttcttctgcctcgtgtaattgacagcaaatgatgcaatgttaaaacatgccttttg---tttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCGGCTGGCACATCATTGCCAG

upper sequence: AT2G47850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G02550.1 (Glycine max), 3'ss of exon 4
--------------gtaagctttgtttccactcatgtcaaataaa--aggctagtctcgagtttgcatgatcttttataaactctttgtagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC
               |     || |   |  |||||| |  || |  |    | | |   | ||  |  ||   || |    | |    ||||||| || ||||||||||||||||| ||||||||||| ||||||||||||||| | |||||||| ||||||||||| |||||||| ||  |  | ||| 
gtttgactcttctttttgctcttctgctcgttcatgttacctacaccaaataaatgtaatgattaaaccatgccttttg---tttaaacagGGTGAGAAAGAATGCTCCTACTATTTAAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCTGCTGGCACATCATTGCCAA

upper sequence: AT2G47850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G17250.1 (Glycine max), 3'ss of exon 4
--------------gtaagctttgtttccactcatgtcaaata-aaaggctagtctcgagtttgcatgatcttttataaactctttgtagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC
               |     || |   ||  ||||| |  || | |   || |    | || |    | | |   |    | |    ||||||| || || |||||||||||||||||||||||||| ||||||||||||||| | |||||||| ||||||||||| |||||||| ||  |  | ||| 
gtatgactcttcgttttgctcttctgctcatccatgttacctacagaaaataatgc--aattggttaaaccatgccttttgtttaaacagGGTGAGAAAGAGTGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCTGCTGGCACATCATTGCCAA

upper sequence: AT2G47850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G02540.1 (Glycine max), 3'ss of exon 4
--------------------gtaagctttgtttccactcatgtcaaataaaaggctagtct-cgagtttgcatgatcttttataaactctttgtagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC
                     |     || ||  | |||  || || | | ||   | | | |||  ||     ||   || |    | |    ||| ||| || ||||||||||||||||||||||| ||||| ||||||| ||||||| | |||||||| ||||||||||| || || || ||  |  | ||| 
gtatgataatggcacttctttttgctcttcttctccctcgcgt-aattgacagcaaattatgcgatgttaagccatgccttttg---tttaaacagGATGAGAAAGAATGCTCCTACTATTTGAAAACAGGGCAGTGCAAATATGGTATATCTTGTAAATTCCATCATCCTCAACCGGCGGGCACATCATTGCCAG

upper sequence: AT2G47850.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0104g01460.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------------gtaagctttgtttccactcatgtcaaataaaaggctagtctcgagtttgcatgatcttttataaactctttg-tagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC
                                                    | ||| | |||   | |   |   |||  |    |    |    ||    | ||   ||  ||| | |     ||||||| || ||||||||||||||||||||||||||||| ||||| ||||||||||| |||||||| ||||||||||| || ||||| ||  |  | ||| 
gttgggatttggtttattcttcaccttttctaatcaaattcgttttactaaatcagcatggttgtaatttggg---aatggacacttccatttagcttatgtttatgaattggaaattttgcaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAGTTTGGTATAACATGTAAATTCCATCATCCTCAACCAGCTGGCACATCATTGCCAG

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|164221125|gb|EL992896.1|EL992896
EST:     GATCCATGAGCCACGTTCCACTAAATATATATGGATACCCTGTACGAGAG                         GGTGATAACGAAT
genomic: GATCCATGAGCCACGTTCCACTAAATATATATGGATACCCTGTACGAGAGgtaagctttg ... ctctttgtagGGTGATAACGAAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcaaataaaaggctagtctcgagtttgcatgatcttttataaactctttgtagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC
                                             ctctttgt  CT-rich tract
                              atgatcttttataaa  TA-rich tract