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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtcagattgctcaagcatttttattttttttgcgttttctcatttatcttacaacgggtttactgaggattttaaatttcttacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA

Basic information

species Arabidopsis thaliana
transcript AT3G03120.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 2
gtaggtcagattgctcaagcattttta---ttttttttgcgttttctcat-ttatcttacaacgg-gtttactgaggattttaaatttct--tacac----agGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
   | |   ||       || ||| |    || |||      | |  ||| | |  || |   |    | | ||| | || |   ||| |  |  ||    ||| ||||||||||||||||| ||||||||||| || || || ||||| |||||||| ||||||||||||||| |||||||  |||||||||||||||||||
---gatattatcatcatggcttttatggggttatttgaaaaatctgacatctcactttgctgggacactgattgatgcttctgcctttgtgctgtaccaccagGGTTCAATGTTGAGAAAGTACAGTACAAGAACGTGATGTTTACAGTATGGGATGTCGGTGGCCAAGAGAAGTTGAGGCCTCTGTGGAGGCATTACTTCAA

upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os10g42940.1 (Oryza sativa), 3'ss of exon 2
gtaggtcagatt---gctcaagcatttttattttttttgcgttttctcatttatcttacaacgggttta-------ctgaggattttaaatttc----ttacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
||||||    |     | |   |    |     |  | |  | || |  ||| | ||    |   |  |       |  |  ||  | |   ||    | |  |||| ||||| || ||||||||||| |||||||||||  | ||||| || ||||||||||||||||| || ||  |||||||||| |||||||| ||||||||
gtaggttcactctcatccctccctccctccgcctcatcgaatcttttattttgttttgagccaaatccaaacccaacctaacatcatcatcatcatcatcatgcagGCTTCAACGTGGAGAAAGTTCAATACAAGAATGTGGTGTTCACTGTGTGGGATGTTGGTGGCCAGGAAAAATTGAGGCCCTTATGGAGGCACTACTTCAA

upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G106795_T03 (Zea mays), 3'ss of exon 2
-----gtaggtcagattgctcaagcatttttattttttttgcgttttctcatttatcttacaa---cgggtttactgaggattttaaatttcttacac-agGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
      |       |  | |  |  |   ||| |     |   | || ||| ||  | | |||   |  || |  |||    | |    | ||   || |||||||||||| ||||||||||| ||||||||||| || || || ||||||||||||||||||||||| ||| ||||||||||||||||||| ||||||||
ccaatatgttcttaaaggttttatgaggattactaaaaataaatgtt-tcactttgcctgcaaattcatgtgtgatgatatctctctgatgctactactagGTTTCAATGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTTTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA

upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G113995_T03 (Zea mays), 3'ss of exon 2
-gtaggtcagattgctcaagcatttttattttttttgcgtttt---ctcatttatcttacaa---cgggtttactgaggattttaaatttcttacac-agGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
     |||  | |    | |||    |  |    || | |||    |  | ||  | | |||   ||  | |   ||    | |    | ||  ||| ||||||||| || ||||||||||| ||||||||||| || || || || |||||||||||||||||||| ||| ||||||||||||||||||| ||||||||
ttcctgtcttaattgaaaggcagggctcctgccattacatttaaaacaaactttccctgcaaattcgtctgtgacgatatgtctctggtgctatcactagGTTTCAACGTCGAGAAAGTTCAATACAAGAATGTGATGTTTACTGTGTGGGATGTTGGTGGCCAAGAAAAGTTGAGGCCCTTGTGGAGGCACTACTTCAA

upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 2
--------------------------------------------------------gtaggtcagattgctcaagcatttttattttttttgcgttttctcatttatcttacaacgggtttactgaggattttaaatttcttacac---agGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
                                                        |    | | | |  || | | | |  |  |    |||  ||    |||  ||     |   ||||| |||     |  | ||| | |||    |||||||||||||||||| ||||| |||||||||||  | ||||| || ||||||||||||||||| |||||||| |||||| |||||||||| ||||||||
gtccgattgtaccacctatctgcttgtgcatttcataacttttggtttcaaccattgctaattacagttgtccaac-tctgcacctgccatgcaattg---attcgtccgttcatatgtttagtgacagcatgcactttatcacattgtagGTTTCAATGTTGAGAAGGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAA

upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
---gtaggtc-agattgctcaagcatttttattttttttgcgttttctcatttatcttacaacgggtttactgaggattttaaatttct-----tacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
   | | ||| | || |     ||     |  ||  |||  |    |  ||   ||| |||    ||||    ||| |||||||||| |         ||||||||||||| |||||||||||||| |||||||| || |||||||| ||||||||||| || |||||||| || |||||  | |||||||| |||||  |
gttgaatgtctatatggtattggcgccgcttgttagttttggccagcaaatgagtct-acataatgtttctctaggtttttaaatttatattgccttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA

upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G01380.2 (Glycine max), 3'ss of exon 3
---------gtaggtcagattgctcaagcatttttattttt-tttgcgttttctcatttatcttacaacgggtttactgaggattttaaatttcttacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
          ||  |   ||||  |  || | ||  ||||    |||   |     |  || ||    |   | |  | |  | |||| ||| | |   ||||||||||||| |||||||||||||| || ||||| || |||||||||||||||||||| || |||||||| || |||||  | |||||||| || || ||
attaagtgtctatatggtattgacctggcttgttagttttggcctgcaaatgagtctacatattgtttctc-tatgtttataaatttatattgcct-tgcagGTTTCAATGTGGAGAAAGTTCAGTATAAAAATGTTATTTTCACAGTTTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTATTTTAA

upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G02110.1 (Glycine max), 3'ss of exon 2
gtaggtcagattgctcaagcatttttattttttttgcgttt--tctcatttatcttacaacgggtttact-gaggattttaaatttct-----tacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
  |      |    |    || ||   |||     | |         |  || | || |    ||||| |  ||| ||    |||| |     |   ||||||| ||||| ||||| |||||||| ||||||||  | ||||| |||||||||||||| || ||||||||  | ||| |  | |||||||| || || ||
caaacatgtaccagtatcacacttaagtttaacaggggaagaactagaaataacctatatgttgtttatttaaggcttacggatttgtagtgctttgcagGTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGGATGTTGGAGGGCAAGAGAAATTAAGGGCACTTTGGAGGCACTATTTTAA

upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G09790.3 (Glycine max), 3'ss of exon 1
gtaggtcagattgctcaagcatttttattttttttgcgttt----tctcatttatcttaca-acgggtttactgaggattttaaatttct-----tacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
 |    |||  | | ||   |  ||||  |         ||        |  || | || | |  | || | | ||| || || |||| |     |   ||||||| ||||| ||||| |||||||| ||||||||  | ||||| |||||||||||||| || ||||||||  | ||| |  | |||||||| || || ||
-tgtaccagtat-cacacttaagtttagctgaggaagaattagaagtagaaataacctatatattgtttgattaaggcttatagatttgtagtgctttgcagGTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGGATGTTGGAGGGCAAGAGAAATTAAGGGCACTTTGGAGGCACTATTTTAA

upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0039g02240.t01 (Vitis vinifera), 3'ss of exon 2
-----gtaggtcagattgctcaagcatttt--tattttttttgcgttttctcatttatcttacaacgggttt--actgaggattttaaatttcttacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
     || | ||| ||||  || | ||| |  |||   | |||   | ||  ||  | |||   |  | |||  | |||  |||||    |  | | | |||||||||||| |||||||||||||| ||||| || || |||||||| |||||||| ||||| |||||||| || |||||  | |||||||||||||| ||
taacagttgatcatattgtacatgtattatactatggatgttgatgtgtcgaatggagcttcagattgattttaattgatcattttctggtaat-atatagGTTTCAATGTGGAGAAAGTTCAGTATAAGAACGTGATGTTCACAGTGTGGGATGTAGGTGGACAAGAGAAACTCAGGCCACTCTGGAGGCATTACTTTAA

upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EDP05355 (Chlamydomonas reinhardtii), 3'ss of exon 1
----gtaggtcagat--tgctcaagcatttttattttttttgcgttttctcatttatct-tacaacgggtttactgaggattttaaatttcttac--acagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
    |||   |||    ||||| |   |     || ||   ||     |  | |   |   |||     |  ||  |    |      | |  ||  ||||| ||||| |||||||| || || |||||||| ||  | ||||| || ||||| || || ||||| ||||||||| ||||  ||||| |||||||||||||
cccagtatcccagcccatgctcca-tgtaccccttattacagcccgaacagaatcccccacacacacaatccacacacacctgcgccctgcaaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGGACGTGGGCGGCCAGGAGAAGCTGCGGCCACTGTGGCGGCATTACTTCAA

upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------gtaggtcagattgctcaagcatttttattttttttgcgttttctcatttatctta---caacgggt-ttactgagg---attttaaatttcttacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
                                                                                  ||     | | || |  | |  | ||   |     | |  |     | | | | |    |||   | || || |     |||||  |||   |   |||| |||||||| ||||||||||| |||||||||||    || ||||| ||||| ||||| |||||||||||  || | ||  ||||| |||||||||||||
gtaatttgacttatcacttgtagtcaatccttcatttttttggtagtgcgcctcttcgtttctgagtatagatggcactgttgttttatacaatgttgcaaccgtatttcctgccaagtgcatgtgagtgtttttgagggtaacatctgttgctaaattacattttccattcaattttcagGGTTCAATGTAGAGAAAGTTCAATACAAGAATGTTGAGTTTACAGTGTGGGACGTTGGAGGCCAAGAGAAATTGCGACCTCTGTGGCGGCATTACTTCAA

upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------gtaggtcagattgctcaagcatttttattttttttgcgttttct---catttatcttacaacgggtt-tactgaggattttaaatttcttaca-------------cagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
                                                                             || |       |  | | | | ||||     ||     | | ||   | || ||    |  | |||| || ||    || |  | ||| |                |||| || ||||| || |||||||| ||||||||||||   |||||||| ||||||||||| || || |||||  || ||||| | ||| |||||||||||||
gtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaatattgtgctgagcgttgatgagtcggctggttatattggcatttgttcacttcctgtgttcccgcatctctcagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA

upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S47_298V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------------------gtaggtcagattgctcaa-gcatttttattttttttgcgttttctcatttatcttacaacgggtttactg--aggattttaaatttct----tacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
                                                                                        | |     ||| |  | | ||| || | | |   | | |     ||||   ||  |    ||    ||  | | | ||    || |    ||  |||| |||||||| |||||||||||||||||||| |||   || ||||| ||||||||||| || ||||||||  || ||||  ||||| ||||||| |||||
gtagcttgacttaacacttccagttgatccttttgtatttgaaagagcccctcttcgtttctgcttatttgatgtatttgcttatttgacggtgttttgtttgatgtattattctgtgtcgagtgctggtgaatttgctttcgaggatgtcatttgttaagttgttgtggttatgcaatattcagGGTTCAATGTGGAGAAAGTTCAGTACAAGAACGTCGAGTTTACAGTGTGGGATGTTGGAGGTCAAGAGAAATTGCGGCCTCTGTGGCGGCATTATTTCAA

upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ08154 (Selaginella moellendorffii), 3'ss of exon 2
gtaggtcagattgctcaagcatttttattttttttgcgttttctcatttatcttacaacgggtttactgaggattttaaatttcttacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
                  | | |  | ||||| | |  | ||  | || |||||    |    || ||       |   | | ||| |  ||| || || || ||||| || ||||||||||||||  | ||||| || |||||||| |||||||| |||||||| || ||  | |||| ||| ||||| | 
------------------gtaatcctttttttctggtttcttggctttcatcttg--gccttcttgctcgactgatgtgaatccttgc-tagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTGGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG

upper sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
gtaggtcagattgctcaagcatttttattttttttgcgttttctcatttatcttacaacg-ggtttactgaggattttaaatttcttacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
              | |  | ||||| |  ||| |  | ||||   || | |||    |  | |||   ||    | | |||  ||| |  ||| || || || ||||| || ||||||||||||||  | ||||| || ||||||||||||||||| |||||||| || ||  | |||| ||| ||||| | 
-------------gtaatccttttttctggtttcttggctttcatcttgaccttcttgctcgatttctcgactgatgtgaatc-cttgc-tagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG

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|164097252|gb|ES191225.1|ES191225
EST:     TACAAGCTCCACATAGGAGAAGTTCTGTCTACTGTTCCCACAATCG                         GTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGG
genomic: TACAAGCTCCACATAGGAGAAGTTCTGTCTACTGTTCCCACAATCGgtaggtcaga ... tcttacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGG
EST: gi|19876194|gb|AU237025.1|AU237025
EST:     ACTATACAAGCTCCACATAGGAGAAGTTCTGTCTACTGTTCCCACAATCG                         GTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGG
genomic: ACTATACAAGCTCCACATAGGAGAAGTTCTGTCTACTGTTCCCACAATCGgtaggtcaga ... tcttacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttctcatttatcttacaacgggtttactgaggattttaaatttcttacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA
                                            ttcttac  putative branch site (score: 2)
                                           tttcttac  CT-rich tract
                                   attttaaatttcttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtcagattgctcaagcatttttattttttttgcgttttctcatttatcttacaacgggtttactgaggattttaaatttcttacacagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG