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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgcaatctaactccctcatgtctttctgcaatgtctcgaaaaaagtcccactaaagttggaacaatttgcagGCGATGATGAAGGACCCATTTGGGAACTATGTAGTGCAGAAGGTTCTTGAAACATGTGATGATCAAAGTCTTGCACTCATTCTTTCTCGCATCAAAGTAC

Basic information

species Arabidopsis thaliana
transcript AT3G10360.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G10360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G123537_T02 (Zea mays), 3'ss of exon 8
-------------------------------------gtctgcaatc--taactccctcatgtctttctgcaatgt----ctcgaaaaa----agtcccactaaagttggaacaatttg-----cagGCGATGATGAAGGACCCATTTGGGAACTATGTAGTGCAGAAGGTTCTTGAAACATGTGATGATCAAAGTCTTGCACTCATTCTTTCTCGCATCAAAGTAC
                                      | |  ||||  ||  ||  |  | |  | |||||   |    |||||   |    ||   ||||     || ||   | ||     ||||| |||||||| ||||  || |  |||||||| |||||||||||||| || ||||||||||| || |  | || | | |||||||| || ||||| || |
gtttgttttcaacattcagtctcatcttgcctttttcttttagaatcggtagttcgatggtctgctgctgcaggattggactcgatgcattctagcaacacttgtaatgtaaacttatgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAGACATGTGATGACCAGAACCGTGAATTGATTCTTTCCCGTATCAAGGTCC

upper sequence: AT3G10360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G32230.1 (Glycine max), 3'ss of exon 11
----------gtctgcaatctaactcc----ctcatgtctttctgca-atgtctcgaa---aaaagtcccactaaa-gttggaa------caatttgcagGCGATGATGAAGGACCCATTTGGGAACTATGTAGTGCAGAAGGTTCTTGAAACATGTGATGATCAAAGTCTTGCACTCATTCTTTCTCGCATCAAAGTAC
           | |   ||  || | |     ||| ||  || || | || | || ||    |   ||  | | || | ||| |      |||||||||||| |||||||||||||| ||||| || ||||| ||||| ||||||||||| || |||||||||| ||||||||  || || |||||||||||||| || |
attccatttatttttttatagaagttcaagtatcaagttgttttgtatatttatcaaatcagaggctcttagtgaatgatggcataacatcaatttgcagGCTATGATGAAGGACCCTTTTGGAAATTATGTTGTGCAAAAGGTTCTTGAGACTTGTGATGATCGAAGTCTTGAGCTGATCCTTTCTCGCATCAAGGTTC

upper sequence: AT3G10360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G35290.1 (Glycine max), 3'ss of exon 11
----------------gtctgcaatctaactccctcatgtctttctgcaatgtctcga--aaaaagtcccactaaa-------gttggaacaatttgcagGCGATGATGAAGGACCCATTTGGGAACTATGTAGTGCAGAAGGTTCTTGAAACATGTGATGATCAAAGTCTTGCACTCATTCTTTCTCGCATCAAAGTAC
                    | | | ||| |  |   |  |||| |  | |      |  | |   ||  | | ||        |   | |||||||||||| |||||||||||||| ||||| || ||||||||||| ||||||||||| || ||||| |||| ||||||||  || || |||||||||||||| || |
attccatttttttttttatagaagtttaagtatcaagttgctttttatatttgtcaaatcagaggctcttagtgaatgatgacataacatcaatttgcagGCTATGATGAAGGACCCTTTTGGAAATTATGTAGTGCAAAAGGTTCTTGAGACTTGTGACGATCGAAGTCTTGAGCTGATCCTTTCTCGCATCAAGGTTC

upper sequence: AT3G10360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv13s0019g04640.t01 (Vitis vinifera), 3'ss of exon 9
-----------------------gtctgca-atctaactccctcatgtctttc-tgcaatgtctcgaaaaaagtcccactaaagttggaacaatttgcagGCGATGATGAAGGACCCATTTGGGAACTATGTAGTGCAGAAGGTTCTTGAAACATGTGATGATCAAAGTCTTGCACTCATTCTTTCTCGCATCAAAGTAC
                          ||   || || ||  |   |   | |  || ||        |   ||   |||| | |       || ||||||   |||||||| ||||||||||| |||||||| ||||| |||||| |||| || ||||||||||| | ||  |   | ||||| ||||||||||| || |
ccctttatgagtaagaggttttaacttgtttatttatctatcctgttcatctagtgaaaaagtgtagactgagcaacactgatgaattgcaaaattgcagATCATGATGAAAGACCCATTTGGAAACTATGTTGTGCAAAAGGTTATTGAGACTTGTGATGATCAGACTCGAGAGTTGATTCTCTCTCGCATCAAGGTCC

upper sequence: AT3G10360.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EDO96479 (Chlamydomonas reinhardtii), 3'ss of exon 1
----------------------------------gtctgcaatctaactccc-tcatgtctttctgcaatgtctcgaaaaaagtcccactaaagttggaacaatt--tgcagGCGATGATGAAGGACCCATTTGGGAACTATGTAGTGCAGAAGGTTCTTGAAACATGTGATGATCAAAGTCTTGCACTCATTCTTTCTCGCATCAAAGTAC
                                  |    |       | |    | ||    ||  |   |   ||         || |    |    |  |     ||||||| |||||||||||||  ||||| ||||| || ||||||||||| || ||    ||    ||  |    |  |   | || ||  | |            
cgcccaccattctgccttccccgccttctgcaccgcgcactgcgcggcactggccctgcaactcccccgcgctccgcctccgcctcctcctccgccacagGACCCGGTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC------------

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|116425116|gb|EG467708.1|EG467708
EST:     TTATACTGATGAAAACGAGCCTCTTCAG                         GCGATGATGAAGGACCCATTTGGGAACTATGTAGTGCAGAAGGTTCTTGAA
genomic: TTATACTGATGAAAACGAGCCTCTTCAGgtctgcaatc ... caatttgcagGCGATGATGAAGGACCCATTTGGGAACTATGTAGTGCAGAAGGTTCTTGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtctttctgcaatgtctcgaaaaaagtcccactaaagttggaacaatttgcagGCGATGATGAAGGACCCATTTGGGAACTATGTAGTGCAGAAGGTTCTTGAAACATGTGATGATCAAAGTCTTGCACTCATTCTTTCTCGCATCAAAGTAC
                               cactaaa  putative branch site (score: 2)
                     aaaaaagt  TA-rich tract