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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgttaatggatccatttaggtggaagcaagaactctgttttttgctctgtttctgctctgcatttctctgtttcactgatgatttgtttgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG

Basic information

species Arabidopsis thaliana
transcript AT3G23810.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os11g26850.2 (Oryza sativa), 3'ss of exon 1
---attgttaatggatccatttaggtggaagcaagaact-ctgttttttgctctgtttctgctctgcatttctctgtttcactgatgatttgtttgcttt--atagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG
   | | ||| || || |        ||||  |  | ||  | | ||||||  || || |    |   |   |  | |  | | |   | |||||  | |  | ||||||||||| |||| || ||||| ||||| || || |||||||||||||||||||| ||||||||||| ||||| |||||||| ||  |||| |||||||
tgaaatattactgaatgctg------ggaattacaatctgttatattttgcaatgattttatcatttttgcttgagatatattaactctgtgtttcttctgaacagTTTGACAACCTGTATGGTTGCCGCCACTCTCTCCCTGATGGTCTCATGAGGGCTACCGATGTTATGATCGCTGGCAAGGTTGCCGTGGTCTGCGGTTATG

upper sequence: AT3G23810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G111909_T01 (Zea mays), 3'ss of exon 2
--attgttaatggatccatttaggtggaagcaagaactctgttttttgctctgtttctgctctgcatttctctgtttcactgatgatttgtttgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG
  | | ||  |   ||   |||     |    || |   || |     |    |       ||    ||  || | |   | ||| ||  |    |||| |||||||||||||||| || ||||| ||||| || || |||||||| |||||||| || || |||||||||||||| |||||||| ||  ||||||| ||||
acaatattttttt-tcttcttataaacagcttagcatgttgctagaaccaaaatccaactactaagattaactatatttat-atgtttcctcctgtttacagTTTGACAACTTGTATGGTTGCCGCCACTCCCTCCCTGATGGTCTGATGAGGGCCACAGACGTTATGATTGCTGGCAAGGTTGCCGTGGTCTGTGGATATG

upper sequence: AT3G23810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G015295_T01 (Zea mays), 3'ss of exon 1
attgttaatggatccatttaggtggaagcaagaactctgttttttgctctgtttctgctct--gcatttctctgtttcactgatg-atttgtttgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG
 ||   |||  ||   | | |     ||   ||  | |   |  | |     |||  || |    | |       || | ||||    || |   ||  | ||||||||||| |||| || ||||| |||||||| || |||||||| |||||||| ||||| |||||||| || ||||||||||| ||  |||| || || |
-ttacaaat--atttttcttgtaaacagtttgacatgttgctagtaccgaaattcaactattaagactaactaaattgattgatatggttctcctctgaacagTTTGACAACCTGTATGGTTGCCGCCACTCGCTCCCTGATGGTCTGATGAGGGCCACTGACGTTATGATCGCCGGAAAGGTTGCCGTGGTCTGCGGATACG

upper sequence: AT3G23810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G11480.1 (Glycine max), 3'ss of exon 1
---------attgttaatggatccatttaggtggaagcaagaactctgttttttgctctgtttctgctctgcatttctctgtttcactgatgatttgtttgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG
           || | ||||||| | ||   |  ||    | | | || ||| |    ||| | |  | ||  |||  |  ||| |    || |||       | | |||||||||||||||| || ||||| ||||| || || |||||||||||||||||||| ||||||||||||||||||||||| |||||| |   ||| ||||
attatactagctggtcatggatctagttgattataatt--ggattttgctttgttgcttgtgttttgtttg--tttaaccttttaatctgtggttt-----tgtaacagTTTGACAACTTGTATGGGTGCCGTCACTCTCTCCCTGATGGTCTCATGAGGGCTACCGATGTTATGATTGCTGGAAAGGTGGCTGTTGTGGCTGGATATG

upper sequence: AT3G23810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G28480.1 (Glycine max), 3'ss of exon 1
attgttaatggatccatttaggtggaagcaagaactctgttttttgctctgtttctgctctgcatttctctgtttcactgatgatttgt----ttgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG
   || | ||| |    |         | |  |    |   ||||||| | || ||    ||   || | | ||   ||  |||| |||    |||  | | ||||||||||||||||||| ||||| ||||| || || |||||||| ||||||||||||||||| ||||||||||||||||| |||||| |   ||| ||||
--ggtcattgggttttgtggatctagtggattatgaattgattttgctttattgct--cgtgttattttttattaaccttttgatctgtggttttgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGGGCTACTGATGTGATGATTGCTGGAAAGGTGGCTGTTGTGGCTGGATATG

upper sequence: AT3G23810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G36620.1 (Glycine max), 3'ss of exon 1
attgttaatggatccatttaggtggaagcaagaactctgttttttgctc-tgtttctgctctgcatttctctgtttcactgatgatttgtttgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG
                     ||     | | |  | | || | || |  | | ||||      |      | |   | || |   |    |   ||  ||||||| |||||||| |||||||| ||||||||||||||||| || ||||| || |||||||| |||||||| |||||||| |||||| | ||||| || |
---------------------gtacgtaccatacattttttgtctgtttgtttgtctgtcggtgaaagaaatataaaagtgtttgatgcaatttgttgcagTTTGATAACTTGTATGGATGCCGTCACTCGCTTCCCGATGGACTGATGAGAGCCACTGATGTGATGATTGCCGGAAAGGTAGCTGTTGTGTGTGGCTACG

upper sequence: AT3G23810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0029g00330.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------------------------------attgtt-aatggatcca-tttaggtggaagcaagaactctgttttt-tgctctgtttctgctctgcatttctctgtttcactgatgatttgtttgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG
                                                    |||||   |||||| | ||| | |      ||||    |  |||| || | ||||| || | ||  ||||| |       |  || | ||  |||   | |||| ||||| ||||| |||||||| || || || || ||||| || ||||| ||||| || || |||||||| ||||||||||| ||| | || || || |
gtattctccagatctgtgatatttgggaattgttttcaacgattcaaccaatttgtttggtggatctagtttggattactagaagagtcgtaattttgtgttttgttt-tgttttgtttttct-taacaattttctgttctggatgcaa-acagTTCGACAATTTGTATGGATGCCGCCATTCACTCCCTGATGGGCTGATGAGAGCTACGGACGTGATGATTGCCGGAAAGGTTGCAGTTGTATGCGGATACG

upper sequence: AT3G23810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv17s0000g09840.t01 (Vitis vinifera), 3'ss of exon 1
-attgttaatggatccatttaggtggaagcaagaactctgttttttgctctgtttctgctctgcatttctctgtttcactgatgat---ttgtttgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG
  |||  |  |  |  |       ||| | || |  | ||  ||| | || ||      |   |  || | ||||  | |  |  |   | || | |  |  |||||||||||||||| |||||||||||||| || ||||||||||||||||| || |||||||| ||||||||||| |||||||||||  ||||||| ||||
acttggcagggtgtggaccc---cggagggaatagttatggattt-gttcagtgctgattgaccccttttatgttctaatatttttcaatggtattcaatgcagTTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGAGCCACTGATGTCATGATTGCTGGCAAGGTTGCTGTGGTCTGTGGGTATG

upper sequence: AT3G23810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S20_229V6.1 (Physcomitrella patens), 3'ss of exon 2
attgttaatg-gatccatttaggtggaagcaagaactctgttttttgctctgtttctgctctgcatttctctgtttcactgatgatttgtttgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG
     ||||| | ||| |    || | |      ||  |   ||| | | || ||      ||  |   |        |||| | || | ||| | |  |||| |||||||||||||| ||||| |||||||| ||||| || || ||||| || || || || |||||||| || ||||||||||| ||||  || || |
----gtaatgtggtccgtgactgtcggat-----acctttcgtttggatgtgatttgatggtgtgtggttgg---cggctgacgcttgggttgttgtgcagTTCGACAACTTGTACGGTTGCCGCCACTCGCTGCCCGACGGCCTGATGAGAGCGACGGACGTGATGATTGCCGGGAAGGTTGCTGTGATCTTCGGGTACG

upper sequence: AT3G23810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S20_291V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------attgttaatggatccatttaggtggaagcaagaactctgttttttgctctgtttctgctctgcatttctctgttt--cactgatgatttgtttgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG
                                   |||||  ||||  | | |  | ||  |   |    | ||     | |  |     |        |    |||      |||| | || | | ||| |  |||| |||||  ||||||| ||||| |||||||| ||||| || || |||||||| || ||||| ||||| || || ||||||||||| ||||  ||||| |
gtaatgtgacccgtgggtggcagattccgtaagtgttgttg-tggacgcgtgtgtg-gggggtgggggggccgtggaacggtaggagggagggggagtgtgtggtgtcgggtgctgacgtttgggtcgctgtgcagTTCGACAATCTGTACGGTTGCCGGCACTCGCTGCCCGACGGGCTGATGAGGGCGACGGATGTGATGATCGCCGGGAAGGTTGCTGTGATCTTCGGTTACG

upper sequence: AT3G23810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ11444 (Selaginella moellendorffii), 3'ss of exon 1
attgttaatggatccatttaggtggaagcaagaactctgttttttgctctgtttctgctctgcatttctctgtttcactgatgatttgtttgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG
                       | |  || ||  ||| || |||  ||| ||       |  | | |||    ||     || |||  ||  |||| |||| |||||| | ||||| ||||||||||| || || ||||| |||||| | || |||||||| ||||| ||||| ||||| || ||  ||  ||| || |
-----------------------gtactcacgacttcttttgtttattctcttgaaaagtt--agtgctca---tcgtgagtgcttttctt--tttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGAGCAACTGATGTGATGATCGCTGGGAAGGTCGCAGTCGTCGCTGGATACG

upper sequence: AT3G23810.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ11220 (Selaginella moellendorffii), 3'ss of exon 1
attgttaatggatccatttaggtggaagcaagaactctgttttttgctctgtttctgctctgcatttctctgtttcactgatgatttgtttgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG
                               | ||||     ||   |   ||  ||   || |    |     |||  |    |   |||  |||| |||| |||||| | ||||| ||||||||||| || || ||||| |||||| | || |||||||| ||||| ||||| ||||| || ||  ||  ||| || |
-------------------------------gtactcacgacttcttttgtttattgtcttgaaaagttagtgctcatcgtgagtgcttttcttttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGAGCAACTGATGTGATGATCGCTGGGAAGGTCGCAGTCGTCGCTGGATACG

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|116474535|gb|EG517127.1|EG517127
EST:     CTCTCTTGTTCCCTGCCATTAACGTCAATGACTCTGTCACCAAGAGCAAG                         TTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGG
genomic: CTCTCTTGTTCCCTGCCATTAACGTCAATGACTCTGTCACCAAGAGCAAGgtaatgtggc ... tgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGG
EST: gi|125198792|gb|EL213746.1|EL213746
EST:     CTCTCTTGTTCCCTGCCATTAACGTCAATGACTCTGTCACCAAGAGCAAG                         TTTGACAACTTG
genomic: CTCTCTTGTTCCCTGCCATTAACGTCAATGACTCTGTCACCAAGAGCAAGgtaatgtggc ... tgctttatagTTTGACAACTTG
EST: gi|86060089|gb|DR355846.1|DR355846
EST:     CTCTCTTGTTCCCTGCCATTAACGTCAATGACTCTGTCACCAAGAGCAAG                         TTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGG
genomic: CTCTCTTGTTCCCTGCCATTAACGTCAATGACTCTGTCACCAAGAGCAAGgtaatgtggc ... tgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGG
EST: gi|116474531|gb|EG517123.1|EG517123
EST:     CTCTCTTGTTCCCTGCCATTAACGTCAATGACTCTGTCACCAAGAGCAAG                         TTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGG
genomic: CTCTCTTGTTCCCTGCCATTAACGTCAATGACTCTGTCACCAAGAGCAAGgtaatgtggc ... tgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGG
EST: gi|116474532|gb|EG517124.1|EG517124
EST:     CTCTCTTGTTCCCTGCCATTAACGTCAATGACTCTGTCACCAAGAGCAAG                         TTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGG
genomic: CTCTCTTGTTCCCTGCCATTAACGTCAATGACTCTGTCACCAAGAGCAAGgtaatgtggc ... tgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGG
EST: gi|116474542|gb|EG517134.1|EG517134
EST:     CTCTCTTGTTCCCTGCCATTAACGTCAATGACTCTGTCACCAAGAGCAAG                         TTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGG
genomic: CTCTCTTGTTCCCTGCCATTAACGTCAATGACTCTGTCACCAAGAGCAAGgtaatgtggc ... tgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGG
EST: gi|116444077|gb|EG486669.1|EG486669
EST:     CTCTCTTGTTCCCTGCCATTAACGTCAATGACTCTGTCACCAAGAGCAAG                         TTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGG
genomic: CTCTCTTGTTCCCTGCCATTAACGTCAATGACTCTGTCACCAAGAGCAAGgtaatgtggc ... tgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctctgtttctgctctgcatttctctgtttcactgatgatttgtttgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG
                              cactgat  putative branch site (score: 3)
                                           tttgcttt  putative PPT
                                      atttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgttaatggatccatttaggtggaagcaagaactctgttttttgctctgtttctgctctgcatttctctgtttcactgatgatttgtttgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - caagaac
- - - - - - - - - - - - - - - - - - - - - - - - ctgtttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatttgt