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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctctcatcattgtccactgtagtttatgaactttctcttcacgtttgacgagtctggcatattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG

Basic information

species Arabidopsis thaliana
transcript AT3G06400.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 11
-----------------------gtaagtctctcatcattgtc--cactgtagtttatgaactttctcttcacgtttgacgagtctggcatattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
                       | |    ||| |       |    |  ||  ||    |||   ||||   ||| ||  |   |||    || |  ||||||||||||||| ||| ||||||||||||||||||| ||||||||||||||||| |||||||||||||| || ||||| |||||||||
gcaagtattcatattgattgtcagcagccttctaacttgcagcggtgccataagttcatgactaattctttttgtt-gataa--ttggtg-gttataacagGAACCCACAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 11
----gtaagtctctcatcattgtccac-----tgtagtttatgaactttctcttcacgtttgacgagt--ctggca-tattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
    |||  |||   |   |||  |||     |||  |||||     | | |      |||      |   |||   | ||    ||||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| |||||||||||||| || || || || ||||||
gtcagtatttctagtagttttgaacacagccatgttatttatatctgtacccaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGTTTTTGTACTGAG

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 11
gtaagtctctca--tcattgtccactgtagtttatgaactttctcttcacg--------tttgacga-gtctggca-tattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
|| ||| | |||  |  || |  |||      | |||  | | |||  ||         ||||  || |  |||   | ||    ||||||||||||||| |||||||| |||||||||||||| ||||||||||||||||| |||||||||||||| || ||||| || ||||||
gtcagtatttcaagtagttatggactcagccatctgatttatatctgtaccaaaattattttgttgatggttggtgcttttacaacagGAACCCACAAGTTGACTTGCAGGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGTACTGAG

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 11
-------------------gtaagtctctcatcattgtccactgtagtttatgaactt---tctcttcacgtttgacgagtctggcatattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
                   || ||   |     |   | || ||  |   || |  |     ||  |    ||||  ||   | |    || |  ||||||||| ||||| ||| ||||||||||||||||||| ||||||||||||||||| |||||||||||||| || ||||| |||||||||
gttagtattcttgttgattgtcagcagccttctaacttgcagtgatgcc-ataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
-----------gtaagtctctcatcattgtccactgtagtttatgaactttctcttcacgtttgacgagtctggcatattctg----------gcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
              | | | |  || || ||   |  | |    |    || |  |    ||| || | |||||   ||              | |||||||| ||||| || |||||||| || |||||||| ||| ||||||||||||| ||||||||||||||||||||||||||||| |||
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgttatattattt-accaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 11
gtaagtctctcatcattgtccactgtagtttatgaactttctcttcacgtttgacgagtctggca--tattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
                        ||| |  || |   ||   |    ||   | |  | | | |  ||| ||| |||||| || |||||||| |||||||| || ||||| || ||| ||||||| || ||||||||||||||||| || ||||| |||||  ||
------------------------gtaata-ataatgatttgttctgagtggcatgtttttagaaattatgctg-cagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG

upper sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 11
gtaagtctctcatcattgtccactgtagtttatgaactttctcttcacgtttgacgagtctggcatattctg--gcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
                        |||   ||  ||   | | |||  |  || |  || |   | ||| ||  ||||||| || |||||||| |||||||| || ||||| || ||| ||||||| || ||||||||||||||||| || ||||| |||||  ||
------------------------gtaa--tagtaatgatttgttc-tgagtggcatgttttagaaattatgctgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG

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|116473628|gb|EG516220.1|EG516220
EST:     GGTATCAATCTTGCTACTGCAGATGTTGTGATCCTTTACGATAGTGATTG                         GAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCN
genomic: GGTATCAATCTTGCTACTGCAGATGTTGTGATCCTTTACGATAGTGATTGgtaagtctct ... attctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCA
EST: gi|164095597|gb|ES023167.1|ES023167
EST:     GTATCAATCTTGCTACTGCAGATGTTGTGATCCTTTACGATAGTGATTG                         GAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGA
genomic: GTATCAATCTTGCTACTGCAGATGTTGTGATCCTTTACGATAGTGATTGgtaagtctct ... attctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtagtttatgaactttctcttcacgtttgacgagtctggcatattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
                           gtttgac  putative branch site (score: 4)
       tttatgaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctctcatcattgtccactgtagtttatgaactttctcttcacgtttgacgagtctggcatattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT