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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcctttgatttggtaaaatctacaatgagttggtagttgtgtaatgccataatgtattataaaacagtatcacattggtccatttatgtgaatttgcagCATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGA

Basic information

species Arabidopsis thaliana
transcript AT4G38510.4
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 7
ctcctttgatttggtaaaatctacaatgagttg-gtagttgtgtaatgccata-atgtatta-taaaacagtatcacattggtccatttatgtgaatttgcagCATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGA
 | || | |  |    |    ||    |  ||| ||| |  |||| |||  || |||| | | ||   |   |||||        |||| ||| ||  |||||  |   || ||||| ||||| || |||||||| || || ||||| ||||||||||| || || ||||| || ||||||||||| || |||||||| || |
-tactgtaaggtcaacattcatatggagcattgtgtattaatgta-tgctttacatgtctaaatatggcttaatcactgcttctgatttttgt-aacctgcagGGTGGTGAAGATGACAACTTTGCTATTGTGTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAATGGTTCCA

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 7
ctcctttgatttggtaaaatctacaatgagttg-gtagttgtgtaatgccata-atgtatta-taaaacagtatcacattggtccatttatgtgaatttgcagCATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGA
 |||| |||  |    |  | ||    |  ||| ||| |  |||| |||  || |||| ||| |||  |    |||| | | ||   || | | |   |||||  |   || ||||| ||||| || |||||||| || || ||||| ||||||||||| || || ||||| || ||||||||||| || ||||| || || |
ttcctgtgaggtcaacatttatatggaggattgtgtattcatgta-tgctttacatgtcttaataaggcttagtcac-tggttctgattttatta-cctgcagGGTGGTGAAGATGACAACTTTGCTATTGTGTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAACGGTTCCA

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 8
ctcctttgatttggtaaaatctacaatgagttggt-agttgtgtaatgccataatgtattataaaacagtatcacattggtccatttatgtgaatttgcagCATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGA
||  |||  ||  |    || |    | | | | | | ||      |    |  |||| | |     |  || | | |  |   |       | | || ||  |   || || || || || || |||||||| ||||| ||||| || ||||||||||||||||| ||||| || ||||| || |||||||||||||| |
cttatttccttcagatttatttttgcttaatcgtttacttaaactctctacttctgtact-tcttgtaagatgaaagtaatttttcacaaatactatgtagGGTGGAGAAGAGGACAATTTTGCTATTGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAA

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 7
ctcctttgatttggtaaaatctacaatgagttggtagttgtgtaatgccataatgtattat----aaaacagtatcacattggtccatttatgtgaatttgcagCATCAGG---AGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGA
      | | |  |   | | |    | | |   |  |||     ||  |   |  | ||     || | |||      |   || | || ||| ||| | |||  |   |   | || || || || ||||||||||| ||||| ||||| || ||||||||||||||||| ||||| |||||||| || ||||| ||||| ||  
-----attaataagcctattttcttcttattcatttattggaacttgttactttacactaagatgaagaaagtggtttttccatctaattttgtcaatatacaggGTGGAGGAGAAGAGGACAATTTTGCCATTGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAAAATGGCTC--

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 7
ctcctttgatttggtaaaatctacaatgagttggt--agttgtgtaatgccataatgtattataaaacagtatcacattggtccatttatgtgaatttgcagCATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGA
         | | |   | |    ||| | ||  |  | || | || | |  || | | || ||| |    |     ||     |  ||      | |||||  |   || || || || || || ||||| || ||||| ||||| || ||||||||||||||||| ||||| |||||||| || |||||||||||||| |
--------gtatagctgactgcttaatcatttacttaaattctttacttctgtacttt-ttgtaagatgaaagtgatttttcaaaaataccatgttatgcagGGTGGAGAAGAGGACAATTTTGCTATTGTATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAA

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 7
ctcctttgatttggtaaaatctacaatgagttggtagttgtgtaatgccataatgtattat----aaaacagtatcacattggtccatttatgtgaatttgcagCATCAG---GAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGA
     || ||  ||  |  | |    | | |   |  |||     ||| |   |  |  |     || | |||      |   || |  | ||| ||| | |||  |      || || || || || ||||| ||||| ||||| ||||| || ||||||||||||||||| ||||| |||||||| || ||||||||||| |   
---aattaataaggctat-tttcttcttattcatttattggaacttgctactttacaccaagatgaagaaagtgatttttcaatcgaactttgtcaatatacagGGTGGAGGAGAAGAGGACAATTTTGCCATCGTGTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCT---

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 7
ctcctttgatttggtaaa-atctacaatgagttggtagttgtgtaatgccataatgtattataaaacagtatcacattggtccatttatgtgaatttgcagCATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGA
     || | |    |   || | |  |   ||     || | |  |   || |  | | |     |  |   | ||   |    |  | | || |||||| ||  ||| || || ||||| |||||||| || ||||| ||||| || ||||||||||||||||| ||||||||||||||||||||||| |||||||| |
-gatgttaaatgaccatttatttcctttttattttattttctttctttttatcaattttgaacttgctatgagatatcatttttctacttttaacttgcagGATGTGGAAGAGGACAACTTTGCCATTGTTTTTGCAGCTATGGGAGTAAACATGGAGACTGCACAGTTTTTTAAACGTGATTTCGAGGAAAATGGATCAA

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 6
ctcctttgatttggtaaaatctacaatgagttggtagttgtgtaatgccataatgtattataaaacagtatcacattggtccatttatgtgaatttgcagCATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGA
                                 |||    |||  | |  | || |  | |       |   | | || |   ||| | |   | | |||| | | |  || || ||||| || || || || ||||| |||||||||||||||||||||||||| ||||| ||| | ||||| ||||| ||||||||||
---------------------------------gtacaattgttttccgtttatcttctgtctgttgttg--agactgatgagtttctttcg-tatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGA

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 6
ctcctttgatttggtaaaatctacaatgagttggtagttgtgtaatgccataatgtattataaaacagtatcacattggtccatttatgtgaatttgcagCATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGA
                                 ||| || |||  | |  | || |  | |       |   | | || |   ||| | |   | | |||| | | |  || || ||||| || || || || ||||| |||||||||||||||||||||||||| ||||| ||| | ||||| ||||| ||||||||||
---------------------------------gtacttttgttttccgtttatcttctgtctgttgttg--agactgatgagtttctttcg-tatccagCGTGATGTTGAAGACAACTTTGCAATCGTCTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGAGATTTTGAGGAAAATGGATCGA

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|124905814|gb|EH979894.1|EH979894
EST:     GTCAGGCTGGTTTGGTTAAGCGTTTAGAGAAGTCAGATAATCTTCTCGAG                         CATCAGGAGGATGATAACTTCG
genomic: GTCAGGCTGGTTTGGTTAAGCGTTTAGAGAAGTCAGATAATCTTCTCGAGgtatcacgat ... gaatttgcagCATCAGGAGGATGATAACTTCG
EST: gi|86066802|gb|DR362559.1|DR362559
EST:     GTCAGGCTGGTTTGGTTAAGCGTTTAGAGAAGTCAGATAATCTTCTCGAG                         CATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAAC
genomic: GTCAGGCTGGTTTGGTTAAGCGTTTAGAGAAGTCAGATAATCTTCTCGAGgtatcacgat ... gaatttgcagCATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAAC
EST: gi|116450411|gb|EG493003.1|EG493003
EST:     GTCAGGCTGGTTTGGTTAAGCGTTTAGAGAAGTCAGATAATCTTCTCGAG                         CATCAGGAGGATGATAACTTCGCCATTGTGTTCGAAGCAATGGGTGTGAAC
genomic: GTCAGGCTGGTTTGGTTAAGCGTTTAGAGAAGTCAGATAATCTTCTCGAGgtatcacgat ... gaatttgcagCATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAAC
EST: gi|124811291|gb|EH896157.1|EH896157
EST:     TAATCTTCTCGAG                         CATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAAC
genomic: TAATCTTCTCGAGgtatcacgat ... gaatttgcagCATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAAC
EST: gi|86066801|gb|DR362558.1|DR362558
EST:     GTCAGGCTGGTTTGGTTAAGCGTTTAGAGAAGTCAGATAATCTTCTCGAG                         CATCAGGAGGATGATAAC
genomic: GTCAGGCTGGTTTGGTTAAGCGTTTAGAGAAGTCAGATAATCTTCTCGAGgtatcacgat ... gaatttgcagCATCAGGAGGATGATAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccataatgtattataaaacagtatcacattggtccatttatgtgaatttgcagCATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGA
     taatgtattataaaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcctttgatttggtaaaatctacaatgagttggtagttgtgtaatgccataatgtattataaaacagtatcacattggtccatttatgtgaatttgcagCATCAGGAGGATGATAACTTCGCCATTGTGTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA