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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaacaatgttacttttgctctttacctaaaaactaacatgttaatttcaaaagcaataacaaaacaagttttgattgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA

Basic information

species Arabidopsis thaliana
transcript AT4G39890.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g09140.1 (Oryza sativa), 3'ss of exon 2
---gtgagaacaatgttacttttgctctttaccta---aaaactaacatgttaatttcaaaagcaataacaaaacaagttttg-----------attgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA
        ||  | |         |  || | |||   ||||||   | |||  ||     || || |||      ||||||            ||    |||||||| ||||| || || || ||| ||||  | ||||||||||||||||| ||||||||||| ||  |  |||| ||||||||  |  
tgaactgaaatcacgcgcacaagacaattcagctagtgaaaactgggaggtt--ttcagctagtaaaaaccgggagagttttatggtgatgataatgtgcagGGATACAGCTGGGCAGGAGAGGTTCCGGAGCTTGATCCCAAGTTACATCAGGGATTCTTCTGTGGCAGTGATTGTTTACGATGTGACTG

upper sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
gtgagaacaatgttacttttgc-tctttacctaaaaactaaca----tgttaatt--------tcaaaagcaat-aacaaaacaa-gttttgattgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA
                     | |   ||  | |    |   |    ||||| ||        |  | | || | | ||   ||  ||| |   ||  ||||||||||| ||||| || || || |||||||| || ||||| |||||||| || |||||||||||  | ||||| || ||||||||||
nnnnnnnnnnnnnnnnnnncacattactatttgagttttggtagctttgttagttcattttcttggagaacagttagcatttcattgttcttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA

upper sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------gtgagaacaatgttac-ttttgctct-ttacctaaaaact------aacatgttaatttcaaaagcaataacaaaacaagttttga-ttgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA
                                                       | | |   || |||  |||  |  | ||   ||   |||      |||   ||  |||  |    || |      ||  |||| | || | ||||||||||| || ||||||||||| || ||||| || ||||| ||||| |||||||||||||||||  ||||||||||||||||| |||
gtaggccatattcctctttaactcatgccacaagacctatttatatttttttttctaaaagttatattagatttcacattgttgtgtaggcactttttttaacccattc-tttgtatgttaaaattgtttcatattttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCA

upper sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 2
------------------------------------------------------------------------gtgagaacaatgttacttttgctctt-tacctaaaaactaacatgttaatttcaaaagcaataa-caaaacaagttttga-ttgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA
                                                                         | | |  |  ||     |||||  | | ||||  |   |   | ||| ||| | ||    | | |  |  |  | || | || | ||||||||||| || ||||||||||| || ||||| || ||||| ||||| |||||||||||||||||  || | ||||| |||||  | |
gtaggatgaattcctcttcaaatcatatatacaagctcagtctttttatatttgtttgtttatttttcaacaattatattagagtgcacattgctggtatgcctagtaggcattgt-ttatttttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATAGTATATGATGTTGCTA

upper sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------gtgagaacaatgttacttttgctctttacctaaaaactaacatgttaatttcaaaagcaataa-caaaacaagttttga-ttgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA
                                                                     | | |  |  ||     |||||  |   |   | |   ||   ||| | | | ||    | | |  |  |  | || | || | ||||||||||| || ||||||||||| || ||||| || ||||| ||||| |||||||||||||||||  || | ||||| |||||  | |
gtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA

upper sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------------gtgagaacaatgttacttttgctctttacctaaaaactaacatgttaatttcaaaagcaataacaaaacaagttttga-ttgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA
                                                                   || | |  |   ||    ||| | | ||   ||    |   |   |  |||  |    || |      |   |||| | || | ||||||||||| || |||||||| || || ||||| || ||||| ||||| |||||||||||||||||  || ||||||| |||||| |||
gtaggccatattcctcttcaactcataccacaagatctatttatatttgtttttttgtattttaaaagttatattagatttcacattgttatgtaggcaattttttttaccgttctttgtatgttaaaagtgtgtcgtattttaacttcacagGGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCA

upper sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 2
---------gtgagaacaatgttacttttgctctttacctaaaaac-taacatgttaat---ttcaaaagcaataacaaaacaagttttga--ttgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA
          | | |    |     ||     || ||  ||      | |  |||| ||    |   |     ||| |       ||||||  || | |||||||||||||| ||||||||||| |||||||| || ||||| ||||| ||||||||||| |||||  |  |||| || |||||    |
gattggtttctcaaattgtttaggtttacatgctgtagatacttgtattatttgtttatatacttctagtttctaaaattttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA

upper sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------gtgagaacaatgt---tacttttgctctttacctaaaaactaacatgttaatttcaaaagcaataacaaaacaagttttgattgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA
                         ||| ||  ||||    ||   | |||  |  |||    ||| || | ||||| |  |  ||||             | || || | |||||||| || ||||||||||||||| |||||||||| || || || ||| | ||||| ||||||||  |  | || || || || || |
tgtggtcttatggggtaagtcgagtgtgggatgaatgcagatatcgtggcttctctcctttttactgacttattaatgttgattgcaaa------------tgtggtt-acagGGATACCGCAGGACAAGAAAGATTCCGGAGTCTAATTCCCAGCTATATCCGTGATTCATCTGTTGCGGTGATCGTCTATGACGTGTCAA

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|116437617|gb|EG480209.1|EG480209
EST:     CTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATG                         GGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAG
genomic: CTATCGAAAACAATGTACCTCGAAGATCGAACAGTTCGTTTGCAGCTATGgtgagaacaa ... tgattgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaactaacatgttaatttcaaaagcaataacaaaacaagttttgattgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA
           atgttaatttcaaaa  TA-rich tract