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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccataatgattattattcttaggattgctctcaagcttctgaactaatacttagtgtgatagaaaatggtgtttatgactcatggaattttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCTTATGGTTTTAAGTCAGATATCTGGTCCTTAG

Basic information

species Arabidopsis thaliana
transcript AT3G44200.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 8
tccataatgattattattcttaggattgctctcaagcttctgaactaat--acttagtgtgatagaaaatggtgtttatgactcatggaattttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCTTATGGTTTTAAGTCAGATATCTGGTCCTTAG
   ||| | ||   | ||      |||  ||| ||  |    ||    |  | ||| | | ||        |     |          |||  | | |||||||||||||||| || || |||||||| || || || ||  | |||||||||||||| || |||||||| ||||||||  | |
--tatagttatctcttttacacacatttatctgaatttgtaaaataggtgaagttattattatttttctatgctcaaactgacagcataatgctttctttagGTTGTTGGAACACCGAATTACATGTGTCCAGAGCTTCTCACAGATATCCCTTATGGATTCAAGTCAGACATCTGGTCTCTTG

upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g64490.1 (Oryza sativa), 3'ss of exon 9
---tccataatgattattat-tcttaggattgctctcaagcttctgaactaatacttagtgtgatagaaaatggtgtttatgactcatggaattttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCTTATGGTTTTAAGTCAGATATCTGGTCCTTAG
     |  | ||||   ||| | ||    | |      |   | | | ||||       | || |   ||||  |  |  |    ||||    ||     ||||||||| ||||| ||||| ||||||||||| || |||||||| || || ||||| || || |||||||| || |||||  | |
tatgtcgaattgatccctatatgttcaagtggaatatcattatgttagctaaatacctttatgttctcaaattcttatattttggcatgatgcttc----ttagGTTGTGGGAACACCAAATTACATGTGCCCAGAGCTGCTTGCAGACATTCCTTACGGATTCAAGTCAGACATATGGTCTCTTG

upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G137118_T02 (Zea mays), 3'ss of exon 9
tccataatgattattattcttaggattgctctcaagcttctgaactaatacttagtgtgatagaaaatggtgtttatgactcatggaa---ttttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCTTATGGTTTTAAGTCAGATATCTGGTCCTTAG
   || |    | |   | |     |   ||||| |      |   ||   | | |||| |     ||       || |||  ||| |   | || | ||||||| || || || ||||| ||||||||||| || ||||| |||||||| || |||||||| |||||||| ||||||||  | |
---atgaaccatgtagatatgctagtccatctcatggaatgtatggaagtgtaattgtgcttttgcattcgtgcaataactggtggcaccatgttttttttagGTGGTCGGGACACCAAATTACATGTGCCCAGAGCTGCTAGCTGATATTCCCTATGGTTTCAAGTCAGACATCTGGTCTCTCG

upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G09910.1 (Glycine max), 3'ss of exon 8
-tccataatgattattattcttaggattgctctcaagcttctgaactaatacttagtgtgatagaaaatggtgtttatgact--catggaattttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCTTATGGTTTTAAGTCAGATATCTGGTCCTTAG
      |||  || | || | || ||||    | |   |  |  || ||||| ||||   |    | ||||  || || | |    |  |  ||| ||| ||||| || |||||||| || ||||||||||| ||||||||||||||||| || ||||| || || || ||||| |||||  |||
gcttccaattttt-taatccatatgattagcgtaacattcatagacaaatacatagtc--accacatatgggattaataattgctgtaaatgtttctatgtagGTGGTAGGAACTCCTAATTACATGTGCCCTGAACTGCTTGCTGATATTCCATATGGATTCAAATCTGATATTTGGTCACTAG

upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 8
tccataatgattattat-tcttaggattgctctcaagctt-ctgaactaatacttagtgtgatagaaaatggtgtttatgactcatggaattttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCTTATGGTTTTAAGTCAGATATCTGGTCCTTAG
|  |  ||||   |  |  | ||  ||| |  |     ||  |  |  |||    ||| |  | |     |  ||| ||   |  |  |  ||| | |  |||| || |||||||| ||||| ||||| || ||||||||||||||||| |||||||| || || || ||||| |||||  |||
tataatatgacattggtaccatatcattaccattgcatttatttcataaatgtgcagt-tactggttgtggaagttaattgatt-taaatatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTGCTTGCTGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG

upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 8
-tccataatgattattattcttaggattgctctcaagcttctgaactaatacttagtgtgatagaaaatggtgtttatgact--catggaattttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCTTATGGTTTTAAGTCAGATATCTGGTCCTTAG
      |||  || | || | |  ||||    | |   |  |  || || || ||||   |    | ||||  || || | |    |  |  ||| |||  |||| || |||||||| || |||||||| || ||||||||||||||||| || ||||| || || || ||||| |||||  | |
gcttccaattttt-taatccatctgattagcgtgacattcatagacaaacacatagtc--accatatatgggattaataattgctgtaaatgtttctatgcagGTGGTAGGAACTCCTAATTACATGTGTCCTGAACTGCTTGCTGATATTCCGTATGGATTCAAATCTGATATTTGGTCACTCG

upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 8
tccataatgattattattcttaggattgctctcaagcttctgaactaatac-ttagtgtgatagaaaatggt-gtttatgactcatggaattttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCTTATGGTTTTAAGTCAGATATCTGGTCCTTAG
     |||  |   | | ||| |   || |   |     | ||  |  ||  || | |  || | | | | |    |||   |     | || | |    |||| ||||||||||| || |||||||| || ||||| ||||| ||||| |||||||| || || || |||||||||||  |||
gttgaaatcttgcctgtgctt-gtcctgttgatat-tcacggacttggtaaatttgagcaatgggacacgctcacctattcatttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG

upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ32716 (Selaginella moellendorffii), 3'ss of exon 8
tccataatgattattattcttaggattgctctcaagcttctgaactaatacttagtgtgatagaaaatggtgtttatgactcatggaattttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCTTATGGTTTTAAGTCAGATATCTGGTCCTTAG
                                             |||    || | || |     |  |  |||   |   |   ||  ||  |    ||| ||||| || ||||| || |||||||||||||| ||||| || ||||| ||||| || || |||||||| ||||| ||||
--------------------------------------------gtaagttctattctgttttggcagcgaatttgacaggaagaaaacattgca----gGTGGTTGGGACCCCAAATTATATGTGCCCGGAACTTCTTGCCGACATCCCATATGGCTTCAAATCAGATATATGGTCGTTAG

upper sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ20709 (Selaginella moellendorffii), 3'ss of exon 8
tccataatgattattattcttaggattgctctcaagcttctgaactaatacttagtgtgatagaaaatggtgtttatgactcatggaattttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCTTATGGTTTTAAGTCAGATATCTGGTCCTTAG
                                             |||    ||   || |     |     |||   |   |   ||  ||  |    ||| ||||| || ||||| || |||||||||||||| ||||| || ||||| ||||| || || |||||||| ||||| ||||
--------------------------------------------gtaagttctatactgttttctcagccaatttgacaggaagaaaacattgca----gGTGGTTGGGACCCCAAATTATATGTGCCCGGAACTTCTTGCCGACATCCCATATGGCTTCAAATCAGATATATGGTCGTTAG

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|86062641|gb|DR358398.1|DR358398
EST:     GGGACTTTGGTCTTGCCAAAACTTTGAAGGCGGATGACCTAACTTCCTCG                         GTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCT
genomic: GGGACTTTGGTCTTGCCAAAACTTTGAAGGCGGATGACCTAACTTCCTCGgtatgttgta ... ttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCT
EST: gi|86062640|gb|DR358397.1|DR358397
EST:     GGGACTTTGGTCTTGCCAAAACTTTGAAGGCGGATGACCTAACTTCCTCG                         GNTGTNGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCT
genomic: GGGACTTTGGTCTTGCCAAAACTTTGAAGGCGGATGACCTAACTTCCTCGgtatgttgta ... ttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCT
EST: gi|86062638|gb|DR358395.1|DR358395
EST:     GGGACTTTGGTCTTGCCAAAACTTTGAAGGCGGATGACCTAACTTCCTCG                         GTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCT
genomic: GGGACTTTGGTCTTGCCAAAACTTTGAAGGCGGATGACCTAACTTCCTCGgtatgttgta ... ttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCT
EST: gi|86062636|gb|DR358393.1|DR358393
EST:     GGGACTTTGGTCTTGCCAAAACTTTGAAGGCGGATGACCTAACTTCCTCG                         GTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCT
genomic: GGGACTTTGGTCTTGCCAAAACTTTGAAGGCGGATGACCTAACTTCCTCGgtatgttgta ... ttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCT
EST: gi|86062639|gb|DR358396.1|DR358396
EST:     GGGACTTTGGTCTTGCCAAAACTTTGAAGGCGGATGACCTAACTTCCTCG                         GTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCT
genomic: GGGACTTTGGTCTTGCCAAAACTTTGAAGGCGGATGACCTAACTTCCTCGgtatgttgta ... ttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCT
EST: gi|86062637|gb|DR358394.1|DR358394
EST:     GGGACTTTGGTCTTGCCAAAACTTTGAAGGCGGATGACCTAACTTCCTCG                         GTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCT
genomic: GGGACTTTGGTCTTGCCAAAACTTTGAAGGCGGATGACCTAACTTCCTCGgtatgttgta ... ttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatacttagtgtgatagaaaatggtgtttatgactcatggaattttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCTTATGGTTTTAAGTCAGATATCTGGTCCTTAG
 aactaat  putative branch site (score: 2)
                                     atggaattttatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccataatgattattattcttaggattgctctcaagcttctgaactaatacttagtgtgatagaaaatggtgtttatgactcatggaattttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCTTATGGTTTTAAGTCAGATATCTGGTCCTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - -tcaagct
- - - - - - - - - - - - - - - - - - - - - aactaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaat